From 60d6239d7e6ce1960964bf8d95026b0414511bd9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Wed, 24 Jun 2026 16:15:16 +0200 Subject: [PATCH 001/102] Add NEXTFLOW_RUN module --- modules/local/nextflow/run/main.nf | 46 ++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 modules/local/nextflow/run/main.nf diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf new file mode 100644 index 0000000..42bc184 --- /dev/null +++ b/modules/local/nextflow/run/main.nf @@ -0,0 +1,46 @@ +process NEXTFLOW_RUN { + + // directives: + tag "$pipeline_name" + + input: + val pipeline_name // String + val nextflow_opts // String + val params_file // pipeline params-file + val samplesheet // pipeline samplesheet + val additional_config // custom configs + val cache_dir // cache directory + + when: + task.ext.when == null || task.ext.when + + exec: + // Set cache directory so workflow can `-resume` + def cache_path = file(cache_dir) + assert cache_path.mkdirs() + // Construct nextflow command + def nxf_cmd = [ + 'nextflow run', + pipeline_name, + nextflow_opts, + params_file ? "-params-file $params_file" : '', + additional_config ? "-c $additional_config" : '', + samplesheet ? "--input $samplesheet" : '', + "--outdir ${task.workDir}/results", + ].join(" ") + // Copy command to shell script in work dir for reference/debugging. + file("$task.workDir/nf-cmd.sh").text = nxf_cmd + // Run nextflow command locally in cache directory + def process = nxf_cmd.execute(null, cache_path.toFile()) + // Print process output to stdout and stderr + process.consumeProcessOutput(System.out, System.err) + process.waitFor() + stdout = process.text + // Copy nextflow log to work directory + cache_path.resolve(".nextflow.log").copyTo("${task.workDir}/nextflow.log") + assert process.exitValue() == 0: stdout + + output: + path "results" , emit: output + val stdout, emit: log +} From bed9bf30998abff06f626aa5e7ec739b8ab81653 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 26 Jun 2026 09:33:15 +0200 Subject: [PATCH 002/102] Add module test and snapshot. --- modules/local/nextflow/run/tests/main.nf.test | 29 ++++ .../nextflow/run/tests/main.nf.test.snap | 155 ++++++++++++++++++ 2 files changed, 184 insertions(+) create mode 100644 modules/local/nextflow/run/tests/main.nf.test create mode 100644 modules/local/nextflow/run/tests/main.nf.test.snap diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test new file mode 100644 index 0000000..5c7232d --- /dev/null +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_process { + + name "Test Process NEXTFLOW_RUN" + script "modules/local/nextflow/run/main.nf" + process "NEXTFLOW_RUN" + + test("Nextflow run nf-core/demo - docker,test") { + + when { + process { + """ + input[0] = 'nf-core/demo' + input[1] = '-ansi-log false -profile docker,test' + input[2] = Channel.value([]) + input[3] = Channel.value([]) + input[4] = Channel.value([]) + input[5] = workflow.workDir.resolve('nf-core/demo').toUriString() + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + +} diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap new file mode 100644 index 0000000..a03c25a --- /dev/null +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -0,0 +1,155 @@ +{ + "Nextflow run nf-core/demo - docker,test": { + "content": [ + { + "0": [ + [ + [ + "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" + ], + [ + [ + "SAMPLE1_PE_1_fastqc.html:md5,957174e1e1fb9c2abd80536a51e577d0", + "SAMPLE1_PE_2_fastqc.html:md5,21d5549235c1585eaf86ce2dd9e4e3d6" + ], + [ + "SAMPLE2_PE_1_fastqc.html:md5,3add6e0615acc08723b157e5a6b7e5b9", + "SAMPLE2_PE_2_fastqc.html:md5,747bbc8a934b8817156e1a166732b8a1" + ], + [ + "SAMPLE3_SE_1_fastqc.html:md5,77c5f0c2e74d7da599f565d9e6094be6", + "SAMPLE3_SE_2_fastqc.html:md5,7a3148ceddfc10d99d2ba0637f28268d" + ] + ], + [ + [ + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" + ], + [ + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" + ], + [ + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" + ] + ], + [ + [ + "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", + "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", + "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", + "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", + "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", + "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", + "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", + "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", + "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", + "llms-full.txt:md5,40078fdd7fbc1b383f7c6597088221df", + "multiqc.log:md5,2e8a964aee376ce9e0ac757ef67328f7", + "multiqc.parquet:md5,46e631b0142d1aea8e98a2a9c82784a4", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_data.json:md5,9e031059c5494162bc45b1fa45e5edac", + "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", + "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", + "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", + "multiqc_sources.txt:md5,5603c75499f875a5ddd75181cc7104ea" + ], + "multiqc_report.html:md5,002fc55c21dca02e22f87b2df8a97dc8" + ], + [ + "execution_report_2026-06-26_09-29-43.html:md5,3dcfa9db5145892e3a8e9c25d1d213c2", + "execution_timeline_2026-06-26_09-29-43.html:md5,a708c0bc85820b245898669a30a3d036", + "execution_trace_2026-06-26_09-29-43.txt:md5,aac839a8dae88a8687b1d9e5e12146f1", + "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", + "params_2026-06-26_09-29-45.json:md5,cd2bb6d7b1104be0ee5a1293085ed941", + "pipeline_dag_2026-06-26_09-29-43.html:md5,4e21647af37ae169f495672d9285c2d1" + ] + ] + ], + "1": [ + "" + ], + "log": [ + "" + ], + "output": [ + [ + [ + "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" + ], + [ + [ + "SAMPLE1_PE_1_fastqc.html:md5,957174e1e1fb9c2abd80536a51e577d0", + "SAMPLE1_PE_2_fastqc.html:md5,21d5549235c1585eaf86ce2dd9e4e3d6" + ], + [ + "SAMPLE2_PE_1_fastqc.html:md5,3add6e0615acc08723b157e5a6b7e5b9", + "SAMPLE2_PE_2_fastqc.html:md5,747bbc8a934b8817156e1a166732b8a1" + ], + [ + "SAMPLE3_SE_1_fastqc.html:md5,77c5f0c2e74d7da599f565d9e6094be6", + "SAMPLE3_SE_2_fastqc.html:md5,7a3148ceddfc10d99d2ba0637f28268d" + ] + ], + [ + [ + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" + ], + [ + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" + ], + [ + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" + ] + ], + [ + [ + "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", + "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", + "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", + "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", + "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", + "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", + "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", + "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", + "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", + "llms-full.txt:md5,40078fdd7fbc1b383f7c6597088221df", + "multiqc.log:md5,2e8a964aee376ce9e0ac757ef67328f7", + "multiqc.parquet:md5,46e631b0142d1aea8e98a2a9c82784a4", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_data.json:md5,9e031059c5494162bc45b1fa45e5edac", + "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", + "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", + "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", + "multiqc_sources.txt:md5,5603c75499f875a5ddd75181cc7104ea" + ], + "multiqc_report.html:md5,002fc55c21dca02e22f87b2df8a97dc8" + ], + [ + "execution_report_2026-06-26_09-29-43.html:md5,3dcfa9db5145892e3a8e9c25d1d213c2", + "execution_timeline_2026-06-26_09-29-43.html:md5,a708c0bc85820b245898669a30a3d036", + "execution_trace_2026-06-26_09-29-43.txt:md5,aac839a8dae88a8687b1d9e5e12146f1", + "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", + "params_2026-06-26_09-29-45.json:md5,cd2bb6d7b1104be0ee5a1293085ed941", + "pipeline_dag_2026-06-26_09-29-43.html:md5,4e21647af37ae169f495672d9285c2d1" + ] + ] + ] + } + ], + "timestamp": "2026-06-26T09:30:30.081888", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } + } +} \ No newline at end of file From 2814025fe2e0f117ae3bea535289c9a13de9fd2f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 09:54:27 +0200 Subject: [PATCH 003/102] Update snapshot to collet output only. --- modules/local/nextflow/run/tests/main.nf.test | 4 +- .../nextflow/run/tests/main.nf.test.snap | 200 ++++++------------ 2 files changed, 64 insertions(+), 140 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index 5c7232d..ed17720 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -21,7 +21,9 @@ nextflow_process { then { assert process.success - assert snapshot(process.out).match() + assert snapshot( + process.out.output[0] //collect { it.collect { file(it).name } } + ).match() } } diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index a03c25a..27f3b60 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -1,152 +1,74 @@ { "Nextflow run nf-core/demo - docker,test": { "content": [ - { - "0": [ + [ + [ + "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" + ], + [ + [ + "SAMPLE1_PE_1_fastqc.html:md5,b8f39b1132e08df4f7156b2f939a5ffd", + "SAMPLE1_PE_2_fastqc.html:md5,b446397d1660841c9ae419a56b68074b" + ], + [ + "SAMPLE2_PE_1_fastqc.html:md5,1fb86bc14c6c395a9f2a135cfd5e1960", + "SAMPLE2_PE_2_fastqc.html:md5,2bbe0772dd3d41edd53fe8a5ad00c952" + ], [ - [ - "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" - ], - [ - [ - "SAMPLE1_PE_1_fastqc.html:md5,957174e1e1fb9c2abd80536a51e577d0", - "SAMPLE1_PE_2_fastqc.html:md5,21d5549235c1585eaf86ce2dd9e4e3d6" - ], - [ - "SAMPLE2_PE_1_fastqc.html:md5,3add6e0615acc08723b157e5a6b7e5b9", - "SAMPLE2_PE_2_fastqc.html:md5,747bbc8a934b8817156e1a166732b8a1" - ], - [ - "SAMPLE3_SE_1_fastqc.html:md5,77c5f0c2e74d7da599f565d9e6094be6", - "SAMPLE3_SE_2_fastqc.html:md5,7a3148ceddfc10d99d2ba0637f28268d" - ] - ], - [ - [ - "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" - ], - [ - "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" - ], - [ - "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" - ] - ], - [ - [ - "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", - "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", - "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", - "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", - "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", - "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", - "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", - "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", - "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", - "llms-full.txt:md5,40078fdd7fbc1b383f7c6597088221df", - "multiqc.log:md5,2e8a964aee376ce9e0ac757ef67328f7", - "multiqc.parquet:md5,46e631b0142d1aea8e98a2a9c82784a4", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_data.json:md5,9e031059c5494162bc45b1fa45e5edac", - "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", - "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", - "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", - "multiqc_sources.txt:md5,5603c75499f875a5ddd75181cc7104ea" - ], - "multiqc_report.html:md5,002fc55c21dca02e22f87b2df8a97dc8" - ], - [ - "execution_report_2026-06-26_09-29-43.html:md5,3dcfa9db5145892e3a8e9c25d1d213c2", - "execution_timeline_2026-06-26_09-29-43.html:md5,a708c0bc85820b245898669a30a3d036", - "execution_trace_2026-06-26_09-29-43.txt:md5,aac839a8dae88a8687b1d9e5e12146f1", - "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", - "params_2026-06-26_09-29-45.json:md5,cd2bb6d7b1104be0ee5a1293085ed941", - "pipeline_dag_2026-06-26_09-29-43.html:md5,4e21647af37ae169f495672d9285c2d1" - ] + "SAMPLE3_SE_1_fastqc.html:md5,5c3c74d38ad82c233e8d810cdff63506", + "SAMPLE3_SE_2_fastqc.html:md5,c1071faf40a0769c0f91a5bf68d73296" ] ], - "1": [ - "" - ], - "log": [ - "" - ], - "output": [ + [ [ - [ - "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" - ], - [ - [ - "SAMPLE1_PE_1_fastqc.html:md5,957174e1e1fb9c2abd80536a51e577d0", - "SAMPLE1_PE_2_fastqc.html:md5,21d5549235c1585eaf86ce2dd9e4e3d6" - ], - [ - "SAMPLE2_PE_1_fastqc.html:md5,3add6e0615acc08723b157e5a6b7e5b9", - "SAMPLE2_PE_2_fastqc.html:md5,747bbc8a934b8817156e1a166732b8a1" - ], - [ - "SAMPLE3_SE_1_fastqc.html:md5,77c5f0c2e74d7da599f565d9e6094be6", - "SAMPLE3_SE_2_fastqc.html:md5,7a3148ceddfc10d99d2ba0637f28268d" - ] - ], - [ - [ - "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" - ], - [ - "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" - ], - [ - "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" - ] - ], - [ - [ - "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", - "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", - "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", - "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", - "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", - "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", - "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", - "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", - "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", - "llms-full.txt:md5,40078fdd7fbc1b383f7c6597088221df", - "multiqc.log:md5,2e8a964aee376ce9e0ac757ef67328f7", - "multiqc.parquet:md5,46e631b0142d1aea8e98a2a9c82784a4", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_data.json:md5,9e031059c5494162bc45b1fa45e5edac", - "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", - "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", - "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", - "multiqc_sources.txt:md5,5603c75499f875a5ddd75181cc7104ea" - ], - "multiqc_report.html:md5,002fc55c21dca02e22f87b2df8a97dc8" - ], - [ - "execution_report_2026-06-26_09-29-43.html:md5,3dcfa9db5145892e3a8e9c25d1d213c2", - "execution_timeline_2026-06-26_09-29-43.html:md5,a708c0bc85820b245898669a30a3d036", - "execution_trace_2026-06-26_09-29-43.txt:md5,aac839a8dae88a8687b1d9e5e12146f1", - "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", - "params_2026-06-26_09-29-45.json:md5,cd2bb6d7b1104be0ee5a1293085ed941", - "pipeline_dag_2026-06-26_09-29-43.html:md5,4e21647af37ae169f495672d9285c2d1" - ] + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" + ], + [ + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" + ], + [ + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" ] + ], + [ + [ + "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", + "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", + "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", + "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", + "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", + "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", + "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", + "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", + "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", + "llms-full.txt:md5,233aaf2cb62a7c9cd273decbe605a81d", + "multiqc.log:md5,fbaf1c02a3465aeff85b5af79dbc4b35", + "multiqc.parquet:md5,ea43f302038252d78d63636502050494", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_data.json:md5,82870c14fc4e70c7ee8acd2f8fe751a6", + "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", + "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", + "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", + "multiqc_sources.txt:md5,62d47e5fc905bbf2a0c9cf153b30e1b1" + ], + "multiqc_report.html:md5,5a459ea005e55b33a1325ee729376405" + ], + [ + "execution_report_2026-06-29_09-53-06.html:md5,3ae0ebaafe0cf727d4cc2ef3538aa6a7", + "execution_timeline_2026-06-29_09-53-06.html:md5,2f41588f0b457d4ca3bd33fcef404c7a", + "execution_trace_2026-06-29_09-53-06.txt:md5,8388a7ae4f961ae1b38e986959eb3c82", + "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", + "params_2026-06-29_09-53-08.json:md5,949bdb63810a36f20a9b5ff18e107e52", + "pipeline_dag_2026-06-29_09-53-06.html:md5,4e21647af37ae169f495672d9285c2d1" ] - } + ] ], - "timestamp": "2026-06-26T09:30:30.081888", + "timestamp": "2026-06-29T09:53:37.049382", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.2" From c1b81b29ef5b450f6176ca391ebb1feeae109f21 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 10:40:18 +0200 Subject: [PATCH 004/102] Update snapshot to collet stable_path and stable_content. --- modules/local/nextflow/run/tests/main.nf.test | 9 +- .../nextflow/run/tests/main.nf.test.snap | 130 +++++++++--------- 2 files changed, 73 insertions(+), 66 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index ed17720..a108700 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -20,9 +20,16 @@ nextflow_process { } then { + def outdir = process.out.output[0] + // stable_path: All files + folders in outdir with a stable path (including file name) + def stable_path = getAllFilesFromDir(outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in outdir with stable content + def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/*.{html,json,txt}', 'multiqc/**']) + assert process.success assert snapshot( - process.out.output[0] //collect { it.collect { file(it).name } } + stable_path, + stable_content, ).match() } diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index 27f3b60..53e74e7 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -2,73 +2,73 @@ "Nextflow run nf-core/demo - docker,test": { "content": [ [ - [ - "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f" - ], - [ - [ - "SAMPLE1_PE_1_fastqc.html:md5,b8f39b1132e08df4f7156b2f939a5ffd", - "SAMPLE1_PE_2_fastqc.html:md5,b446397d1660841c9ae419a56b68074b" - ], - [ - "SAMPLE2_PE_1_fastqc.html:md5,1fb86bc14c6c395a9f2a135cfd5e1960", - "SAMPLE2_PE_2_fastqc.html:md5,2bbe0772dd3d41edd53fe8a5ad00c952" - ], - [ - "SAMPLE3_SE_1_fastqc.html:md5,5c3c74d38ad82c233e8d810cdff63506", - "SAMPLE3_SE_2_fastqc.html:md5,c1071faf40a0769c0f91a5bf68d73296" - ] - ], - [ - [ - "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a" - ], - [ - "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10" - ], - [ - "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" - ] - ], - [ - [ - "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", - "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", - "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", - "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", - "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", - "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", - "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", - "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", - "fastqc_top_overrepresented_sequences_table.txt:md5,c3e4443681ebb6cea6bb2f1b63a0072c", - "llms-full.txt:md5,233aaf2cb62a7c9cd273decbe605a81d", - "multiqc.log:md5,fbaf1c02a3465aeff85b5af79dbc4b35", - "multiqc.parquet:md5,ea43f302038252d78d63636502050494", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_data.json:md5,82870c14fc4e70c7ee8acd2f8fe751a6", - "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", - "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78", - "multiqc_software_versions.txt:md5,97e94f53ceb84d4684be0e89c58adf70", - "multiqc_sources.txt:md5,62d47e5fc905bbf2a0c9cf153b30e1b1" - ], - "multiqc_report.html:md5,5a459ea005e55b33a1325ee729376405" - ], - [ - "execution_report_2026-06-29_09-53-06.html:md5,3ae0ebaafe0cf727d4cc2ef3538aa6a7", - "execution_timeline_2026-06-29_09-53-06.html:md5,2f41588f0b457d4ca3bd33fcef404c7a", - "execution_trace_2026-06-29_09-53-06.txt:md5,8388a7ae4f961ae1b38e986959eb3c82", - "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48", - "params_2026-06-29_09-53-08.json:md5,949bdb63810a36f20a9b5ff18e107e52", - "pipeline_dag_2026-06-29_09-53-06.html:md5,4e21647af37ae169f495672d9285c2d1" - ] + "", + "cowpy", + "cowpy/cowpy.txt", + "fastqc", + "fastqc/SAMPLE1_PE", + "fastqc/SAMPLE1_PE/SAMPLE1_PE_1_fastqc.html", + "fastqc/SAMPLE1_PE/SAMPLE1_PE_2_fastqc.html", + "fastqc/SAMPLE2_PE", + "fastqc/SAMPLE2_PE/SAMPLE2_PE_1_fastqc.html", + "fastqc/SAMPLE2_PE/SAMPLE2_PE_2_fastqc.html", + "fastqc/SAMPLE3_SE", + "fastqc/SAMPLE3_SE/SAMPLE3_SE_1_fastqc.html", + "fastqc/SAMPLE3_SE/SAMPLE3_SE_2_fastqc.html", + "fq", + "fq/SAMPLE1_PE", + "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R1.fastq.gz", + "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R2.fastq.gz", + "fq/SAMPLE2_PE", + "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R1.fastq.gz", + "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R2.fastq.gz", + "fq/SAMPLE3_SE", + "fq/SAMPLE3_SE/SAMPLE3_SE_sample1_R1.fastq.gz", + "fq/SAMPLE3_SE/SAMPLE3_SE_sample2_R1.fastq.gz", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_demo_software_mqc_versions.yml" + ], + [ + "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f", + "SAMPLE1_PE_1_fastqc.html:md5,b8f39b1132e08df4f7156b2f939a5ffd", + "SAMPLE1_PE_2_fastqc.html:md5,b446397d1660841c9ae419a56b68074b", + "SAMPLE2_PE_1_fastqc.html:md5,1fb86bc14c6c395a9f2a135cfd5e1960", + "SAMPLE2_PE_2_fastqc.html:md5,2bbe0772dd3d41edd53fe8a5ad00c952", + "SAMPLE3_SE_1_fastqc.html:md5,5c3c74d38ad82c233e8d810cdff63506", + "SAMPLE3_SE_2_fastqc.html:md5,c1071faf40a0769c0f91a5bf68d73296", + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a", + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10", + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48" ] ], - "timestamp": "2026-06-29T09:53:37.049382", + "timestamp": "2026-06-29T10:40:06.455663", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.2" From 93b17a63843c007be6bb0b8722c09bd0aea514b8 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 10:45:05 +0200 Subject: [PATCH 005/102] Update changelog. --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a327c2c..51e22ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` +- `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. + ### `Fixed` ### `Dependencies` From 447aee644d4e5ad6fe423e61c9fbefd287f3a28f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 10:46:37 +0200 Subject: [PATCH 006/102] Update changelog. --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 51e22ee..e8e704c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` -- `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. +- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. ### `Fixed` From b13793370e2ab0c1bd279d45d884e634550d73bf Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 10:53:29 +0200 Subject: [PATCH 007/102] Update implementation to have flexible outdir. --- modules/local/nextflow/run/main.nf | 5 +++-- modules/local/nextflow/run/tests/main.nf.test | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index 42bc184..b109e9c 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -10,6 +10,7 @@ process NEXTFLOW_RUN { val samplesheet // pipeline samplesheet val additional_config // custom configs val cache_dir // cache directory + val outdir // output directory when: task.ext.when == null || task.ext.when @@ -26,7 +27,7 @@ process NEXTFLOW_RUN { params_file ? "-params-file $params_file" : '', additional_config ? "-c $additional_config" : '', samplesheet ? "--input $samplesheet" : '', - "--outdir ${task.workDir}/results", + "--outdir ${task.workDir}/$outdir", ].join(" ") // Copy command to shell script in work dir for reference/debugging. file("$task.workDir/nf-cmd.sh").text = nxf_cmd @@ -41,6 +42,6 @@ process NEXTFLOW_RUN { assert process.exitValue() == 0: stdout output: - path "results" , emit: output + path outdir , emit: output val stdout, emit: log } diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index a108700..b4cb726 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { input[3] = Channel.value([]) input[4] = Channel.value([]) input[5] = workflow.workDir.resolve('nf-core/demo').toUriString() + input[6] = 'results' """ } } From 5e9c171cca691051a95dab96049033118e0e5cfe Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 11:00:57 +0200 Subject: [PATCH 008/102] Update test to not snapshot unstable file. --- modules/local/nextflow/run/tests/main.nf.test | 2 +- modules/local/nextflow/run/tests/main.nf.test.snap | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index b4cb726..f15596c 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -25,7 +25,7 @@ nextflow_process { // stable_path: All files + folders in outdir with a stable path (including file name) def stable_path = getAllFilesFromDir(outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in outdir with stable content - def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/*.{html,json,txt}', 'multiqc/**']) + def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/**', 'multiqc/**']) assert process.success assert snapshot( diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index 53e74e7..d2eb9ff 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -64,11 +64,10 @@ "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10", "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", - "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", - "nf_core_demo_software_mqc_versions.yml:md5,74326c85ce13ec18c2e46093f80c5f48" + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" ] ], - "timestamp": "2026-06-29T10:40:06.455663", + "timestamp": "2026-06-29T10:58:05.668915", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.2" From cef23c7db6a2cdee4855fd0d08689b29ea16595d Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 11:26:47 +0200 Subject: [PATCH 009/102] Fix revision in test. --- modules/local/nextflow/run/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index f15596c..b43b6ed 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_process { process { """ input[0] = 'nf-core/demo' - input[1] = '-ansi-log false -profile docker,test' + input[1] = '-ansi-log false -profile docker,test -revision 1.2.0' input[2] = Channel.value([]) input[3] = Channel.value([]) input[4] = Channel.value([]) From 779d06eef161ddb681865b1dc68f5a7aaf974ea0 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 11:46:50 +0200 Subject: [PATCH 010/102] Revert flexible outdir feature. --- modules/local/nextflow/run/main.nf | 5 ++--- modules/local/nextflow/run/tests/main.nf.test | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index b109e9c..42bc184 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -10,7 +10,6 @@ process NEXTFLOW_RUN { val samplesheet // pipeline samplesheet val additional_config // custom configs val cache_dir // cache directory - val outdir // output directory when: task.ext.when == null || task.ext.when @@ -27,7 +26,7 @@ process NEXTFLOW_RUN { params_file ? "-params-file $params_file" : '', additional_config ? "-c $additional_config" : '', samplesheet ? "--input $samplesheet" : '', - "--outdir ${task.workDir}/$outdir", + "--outdir ${task.workDir}/results", ].join(" ") // Copy command to shell script in work dir for reference/debugging. file("$task.workDir/nf-cmd.sh").text = nxf_cmd @@ -42,6 +41,6 @@ process NEXTFLOW_RUN { assert process.exitValue() == 0: stdout output: - path outdir , emit: output + path "results" , emit: output val stdout, emit: log } diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index b43b6ed..e3acfae 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -15,7 +15,6 @@ nextflow_process { input[3] = Channel.value([]) input[4] = Channel.value([]) input[5] = workflow.workDir.resolve('nf-core/demo').toUriString() - input[6] = 'results' """ } } @@ -27,6 +26,7 @@ nextflow_process { // stable_content: All files in outdir with stable content def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/**', 'multiqc/**']) + assert process.success assert snapshot( stable_path, From f87c4cbe1ce3306eac55080c3c7df699234391f6 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 12:10:02 +0200 Subject: [PATCH 011/102] Update test to capture software versions. --- modules/local/nextflow/run/tests/main.nf.test | 5 ++++- .../local/nextflow/run/tests/main.nf.test.snap | 18 ++++++++++++++++-- 2 files changed, 20 insertions(+), 3 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index e3acfae..30a8a71 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -26,10 +26,13 @@ nextflow_process { // stable_content: All files in outdir with stable content def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/**', 'multiqc/**']) - assert process.success assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("${outdir}/pipeline_info/nf_core_demo_software_mqc_versions.yml"), + // All stable path name, with a relative path stable_path, + // All files with stable contents stable_content, ).match() } diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index d2eb9ff..7ef3278 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -1,6 +1,20 @@ { "Nextflow run nf-core/demo - docker,test": { "content": [ + { + "COWPY": { + "cowpy": "1.1.5" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "SEQTK_TRIM": { + "seqtk": "1.4-r122" + }, + "Workflow": { + "nf-core/demo": "v1.2.0-g32893af" + } + }, [ "", "cowpy", @@ -67,10 +81,10 @@ "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" ] ], - "timestamp": "2026-06-29T10:58:05.668915", + "timestamp": "2026-06-29T12:09:35.915307", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.2" + "nextflow": "25.10.4" } } } \ No newline at end of file From 2e4665d98290721640aab4ad3cf62ad47455cc61 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 13:43:23 +0200 Subject: [PATCH 012/102] Update snapshots with arm64. --- .../nextflow/run/tests/main.nf.test.snap | 44 ++++++++++++++++++- 1 file changed, 42 insertions(+), 2 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index 7ef3278..695fa29 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -61,6 +61,46 @@ "multiqc/multiqc_data/multiqc_general_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_demo_software_mqc_versions.yml" @@ -81,10 +121,10 @@ "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" ] ], - "timestamp": "2026-06-29T12:09:35.915307", + "timestamp": "2026-06-29T12:24:29.271329", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.4" } } } \ No newline at end of file From 025046acd2a7785e366291cc85fec4a3efbe8612 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 14:01:09 +0200 Subject: [PATCH 013/102] Add main workflow with NFCORE_ONCOANALYSER. --- main.nf | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/main.nf b/main.nf index 47a59d9..22be0eb 100644 --- a/main.nf +++ b/main.nf @@ -12,6 +12,7 @@ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "./modules/local/nextflow/run/main" /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -25,6 +26,19 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +workflow { + + + NFCORE_ONCOANALYSER( + 'nf-core/oncoanalyser', + params.nextflow_opts, + params.params_file, + ch_samplesheet, + params.additional_config, + params.cache_dir + ) + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From cdccf51ed8eb90a5e8b532bf08ed5787b8cb9465 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 14:09:06 +0200 Subject: [PATCH 014/102] Add input parameters. --- nextflow.config | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index dc433e3..cca786e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,9 +9,12 @@ // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags - // Input options - input = null + // Oncoanalyser input parameters + oncoanalyser.nextflow_opts = null + oncoanalyser.params_file = null + oncoanalyser.samplesheet = null + oncoanalyser.additional_config = null + oncoanalyser.cache_dir = null // Boilerplate options outdir = null From 69a9e55a6b10513050164437e3ad16bdb6fec613 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 14:10:47 +0200 Subject: [PATCH 015/102] Update main.nf --- main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index 22be0eb..41fade0 100644 --- a/main.nf +++ b/main.nf @@ -31,11 +31,11 @@ workflow { NFCORE_ONCOANALYSER( 'nf-core/oncoanalyser', - params.nextflow_opts, - params.params_file, - ch_samplesheet, - params.additional_config, - params.cache_dir + params.oncoanalyser.nextflow_opts, + params.oncoanalyser.params_file, + params.oncoanalyser.samplesheet, + params.oncoanalyser.additional_config, + params.oncoanalyser.cache_dir, ) } From e4fa06b36388c7bd803dba3f0a7d343031e9b800 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 14:11:00 +0200 Subject: [PATCH 016/102] Update test config --- conf/test.config | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/conf/test.config b/conf/test.config index 74c7407..e10a350 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,8 +22,10 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + // Oncoanalyser input parameters + oncoanalyser.nextflow_opts = '-profile test,docker' + oncoanalyser.params_file = null + oncoanalyser.samplesheet = null + oncoanalyser.additional_config = null + oncoanalyser.cache_dir = null } From 6a98cdbd2aee63c7140628610792c62c4de45b3a Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 14:45:04 +0200 Subject: [PATCH 017/102] Update default parameters to match val variable type. --- conf/test.config | 10 +++++----- nextflow.config | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/conf/test.config b/conf/test.config index e10a350..0064ee5 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,9 +23,9 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = '-profile test,docker' - oncoanalyser.params_file = null - oncoanalyser.samplesheet = null - oncoanalyser.additional_config = null - oncoanalyser.cache_dir = null + oncoanalyser.nextflow_opts = '-profile test,docker' + oncoanalyser.params_file = '' + oncoanalyser.samplesheet = '' + oncoanalyser.additional_config = '' + oncoanalyser.cache_dir = '' } diff --git a/nextflow.config b/nextflow.config index cca786e..173466a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,11 +10,11 @@ params { // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = null - oncoanalyser.params_file = null - oncoanalyser.samplesheet = null - oncoanalyser.additional_config = null - oncoanalyser.cache_dir = null + oncoanalyser.nextflow_opts = '' + oncoanalyser.params_file = '' + oncoanalyser.samplesheet = '' + oncoanalyser.additional_config = '' + oncoanalyser.cache_dir = '' // Boilerplate options outdir = null From 56e73ff305e97a98a3d00e3e3bdfb16c9d361db8 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Mon, 29 Jun 2026 16:14:04 +0200 Subject: [PATCH 018/102] feat: Add `NEXTFLOW_RUN` local module (#2) ### Added - `NEXTFLOW_RUN` local module based on based on [`mahesh-panchal/nf-cascade`](https://github.com/mahesh-panchal/nf-cascade). --- CHANGELOG.md | 2 + modules/local/nextflow/run/main.nf | 46 +++++++ modules/local/nextflow/run/tests/main.nf.test | 42 ++++++ .../nextflow/run/tests/main.nf.test.snap | 130 ++++++++++++++++++ 4 files changed, 220 insertions(+) create mode 100644 modules/local/nextflow/run/main.nf create mode 100644 modules/local/nextflow/run/tests/main.nf.test create mode 100644 modules/local/nextflow/run/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index a327c2c..e8e704c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` +- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. + ### `Fixed` ### `Dependencies` diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf new file mode 100644 index 0000000..42bc184 --- /dev/null +++ b/modules/local/nextflow/run/main.nf @@ -0,0 +1,46 @@ +process NEXTFLOW_RUN { + + // directives: + tag "$pipeline_name" + + input: + val pipeline_name // String + val nextflow_opts // String + val params_file // pipeline params-file + val samplesheet // pipeline samplesheet + val additional_config // custom configs + val cache_dir // cache directory + + when: + task.ext.when == null || task.ext.when + + exec: + // Set cache directory so workflow can `-resume` + def cache_path = file(cache_dir) + assert cache_path.mkdirs() + // Construct nextflow command + def nxf_cmd = [ + 'nextflow run', + pipeline_name, + nextflow_opts, + params_file ? "-params-file $params_file" : '', + additional_config ? "-c $additional_config" : '', + samplesheet ? "--input $samplesheet" : '', + "--outdir ${task.workDir}/results", + ].join(" ") + // Copy command to shell script in work dir for reference/debugging. + file("$task.workDir/nf-cmd.sh").text = nxf_cmd + // Run nextflow command locally in cache directory + def process = nxf_cmd.execute(null, cache_path.toFile()) + // Print process output to stdout and stderr + process.consumeProcessOutput(System.out, System.err) + process.waitFor() + stdout = process.text + // Copy nextflow log to work directory + cache_path.resolve(".nextflow.log").copyTo("${task.workDir}/nextflow.log") + assert process.exitValue() == 0: stdout + + output: + path "results" , emit: output + val stdout, emit: log +} diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test new file mode 100644 index 0000000..4c94b71 --- /dev/null +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -0,0 +1,42 @@ +nextflow_process { + + name "Test Process NEXTFLOW_RUN" + script "modules/local/nextflow/run/main.nf" + process "NEXTFLOW_RUN" + + test("Nextflow run nf-core/demo - docker,test") { + + when { + process { + """ + input[0] = 'nf-core/demo' + input[1] = '-ansi-log false -profile docker,test -revision 1.2.0' + input[2] = '' + input[3] = '' + input[4] = '' + input[5] = workflow.workDir.resolve('nf-core/demo').toUriString() + """ + } + } + + then { + def outdir = process.out.output[0] + // stable_path: All files + folders in outdir with a stable path (including file name) + def stable_path = getAllFilesFromDir(outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in outdir with stable content + def stable_content = getAllFilesFromDir(outdir, ignore: ['pipeline_info/**', 'multiqc/**']) + + assert process.success + assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("${outdir}/pipeline_info/nf_core_demo_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content, + ).match() + } + + } + +} diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap new file mode 100644 index 0000000..695fa29 --- /dev/null +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -0,0 +1,130 @@ +{ + "Nextflow run nf-core/demo - docker,test": { + "content": [ + { + "COWPY": { + "cowpy": "1.1.5" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "SEQTK_TRIM": { + "seqtk": "1.4-r122" + }, + "Workflow": { + "nf-core/demo": "v1.2.0-g32893af" + } + }, + [ + "", + "cowpy", + "cowpy/cowpy.txt", + "fastqc", + "fastqc/SAMPLE1_PE", + "fastqc/SAMPLE1_PE/SAMPLE1_PE_1_fastqc.html", + "fastqc/SAMPLE1_PE/SAMPLE1_PE_2_fastqc.html", + "fastqc/SAMPLE2_PE", + "fastqc/SAMPLE2_PE/SAMPLE2_PE_1_fastqc.html", + "fastqc/SAMPLE2_PE/SAMPLE2_PE_2_fastqc.html", + "fastqc/SAMPLE3_SE", + "fastqc/SAMPLE3_SE/SAMPLE3_SE_1_fastqc.html", + "fastqc/SAMPLE3_SE/SAMPLE3_SE_2_fastqc.html", + "fq", + "fq/SAMPLE1_PE", + "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R1.fastq.gz", + "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R2.fastq.gz", + "fq/SAMPLE2_PE", + "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R1.fastq.gz", + "fq/SAMPLE2_PE/SAMPLE2_PE_sample2_R2.fastq.gz", + "fq/SAMPLE3_SE", + "fq/SAMPLE3_SE/SAMPLE3_SE_sample1_R1.fastq.gz", + "fq/SAMPLE3_SE/SAMPLE3_SE_sample2_R1.fastq.gz", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_demo_software_mqc_versions.yml" + ], + [ + "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f", + "SAMPLE1_PE_1_fastqc.html:md5,b8f39b1132e08df4f7156b2f939a5ffd", + "SAMPLE1_PE_2_fastqc.html:md5,b446397d1660841c9ae419a56b68074b", + "SAMPLE2_PE_1_fastqc.html:md5,1fb86bc14c6c395a9f2a135cfd5e1960", + "SAMPLE2_PE_2_fastqc.html:md5,2bbe0772dd3d41edd53fe8a5ad00c952", + "SAMPLE3_SE_1_fastqc.html:md5,5c3c74d38ad82c233e8d810cdff63506", + "SAMPLE3_SE_2_fastqc.html:md5,c1071faf40a0769c0f91a5bf68d73296", + "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a", + "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", + "SAMPLE2_PE_sample2_R2.fastq.gz:md5,63d5e4ac37927c2ecec4b74d2ff99a10", + "SAMPLE3_SE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", + "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" + ] + ], + "timestamp": "2026-06-29T12:24:29.271329", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.4" + } + } +} \ No newline at end of file From cdab1c16d696758f80393d38944dd6a7aa6eda1d Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 17:59:52 +0200 Subject: [PATCH 019/102] Update setting for cache_dir. --- main.nf | 2 +- modules/local/nextflow/run/main.nf | 8 ++++---- nextflow.config | 1 - 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 41fade0..7f9d774 100644 --- a/main.nf +++ b/main.nf @@ -35,7 +35,7 @@ workflow { params.oncoanalyser.params_file, params.oncoanalyser.samplesheet, params.oncoanalyser.additional_config, - params.oncoanalyser.cache_dir, + workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) } diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index 42bc184..e33e5a0 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -11,6 +11,10 @@ process NEXTFLOW_RUN { val additional_config // custom configs val cache_dir // cache directory + output: + path "results" , emit: output + val stdout, emit: log + when: task.ext.when == null || task.ext.when @@ -39,8 +43,4 @@ process NEXTFLOW_RUN { // Copy nextflow log to work directory cache_path.resolve(".nextflow.log").copyTo("${task.workDir}/nextflow.log") assert process.exitValue() == 0: stdout - - output: - path "results" , emit: output - val stdout, emit: log } diff --git a/nextflow.config b/nextflow.config index b6739d6..35462cd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,6 @@ params { oncoanalyser.params_file = '' oncoanalyser.samplesheet = '' oncoanalyser.additional_config = '' - oncoanalyser.cache_dir = '' // Boilerplate options publish_dir_mode = 'copy' From 6b549fa53252cdbda063f29a04e95f4e47f1eab3 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 18:00:50 +0200 Subject: [PATCH 020/102] Fix linting issue with block order in NEXTFLOW_RUN. --- modules/local/nextflow/run/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index 42bc184..e33e5a0 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -11,6 +11,10 @@ process NEXTFLOW_RUN { val additional_config // custom configs val cache_dir // cache directory + output: + path "results" , emit: output + val stdout, emit: log + when: task.ext.when == null || task.ext.when @@ -39,8 +43,4 @@ process NEXTFLOW_RUN { // Copy nextflow log to work directory cache_path.resolve(".nextflow.log").copyTo("${task.workDir}/nextflow.log") assert process.exitValue() == 0: stdout - - output: - path "results" , emit: output - val stdout, emit: log } From c18879a7bcdd6cc533ae13dd225d14578eea57ce Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 18:02:41 +0200 Subject: [PATCH 021/102] Remove cache_dir parameter from test.config. --- conf/test.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 0064ee5..db7d46a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -27,5 +27,4 @@ params { oncoanalyser.params_file = '' oncoanalyser.samplesheet = '' oncoanalyser.additional_config = '' - oncoanalyser.cache_dir = '' } From 32350c5163f426949de24ec5a079c577ec31e7d2 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 29 Jun 2026 18:08:37 +0200 Subject: [PATCH 022/102] Update pipeline test to match output directory strategy. --- tests/default.nf.test | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 4e6c99f..14a456a 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -6,22 +6,15 @@ nextflow_pipeline { test("-profile test") { - when { - params { - outdir = "$outputDir" - } - } - then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir($outputDir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_content = getAllFilesFromDir($outputDir, ignoreFile: 'tests/.nftignore') + assert workflow.success assertAll( { assert snapshot( - // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/oncoflow_software_mqc_versions.yml"), // All stable path name, with a relative path stable_path, // All files with stable contents From ce915c4f641cd3963bf46b8d8fc2a220a2e08981 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 30 Jun 2026 09:39:34 +0200 Subject: [PATCH 023/102] Update test profile to use stub. --- conf/test.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index db7d46a..5f0fad6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,11 +19,11 @@ process { } params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + config_profile_name = 'Test profile - stub' + config_profile_description = 'Minimal stub test to check if both pipelines are run sequentially' // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = '-profile test,docker' + oncoanalyser.nextflow_opts = '-profile test,docker -stub' oncoanalyser.params_file = '' oncoanalyser.samplesheet = '' oncoanalyser.additional_config = '' From 2a2e26ae3b37e1e7828f391c53cdba6a127baa06 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 30 Jun 2026 09:39:47 +0200 Subject: [PATCH 024/102] Remove unnecessary new line in main.nf --- main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/main.nf b/main.nf index 7f9d774..ecf1bcd 100644 --- a/main.nf +++ b/main.nf @@ -28,7 +28,6 @@ include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "./modules/local/nextflow/r workflow { - NFCORE_ONCOANALYSER( 'nf-core/oncoanalyser', params.oncoanalyser.nextflow_opts, From 1f22805b06636377950f7553c285872bd0f0134f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 30 Jun 2026 11:57:35 +0200 Subject: [PATCH 025/102] Update test config. --- conf/test.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index 5f0fad6..3d54b76 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,11 +19,11 @@ process { } params { - config_profile_name = 'Test profile - stub' - config_profile_description = 'Minimal stub test to check if both pipelines are run sequentially' + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test to check if both pipelines are run sequentially' // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = '-profile test,docker -stub' + oncoanalyser.nextflow_opts = '-profile test,docker' oncoanalyser.params_file = '' oncoanalyser.samplesheet = '' oncoanalyser.additional_config = '' From 6548d13c8fec05b7f2c3a6dcc24a85c8b1b3a035 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 30 Jun 2026 12:12:34 +0200 Subject: [PATCH 026/102] Update pipeline test to match output directory strategy. --- tests/default.nf.test | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 14a456a..3d5b36e 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -7,9 +7,9 @@ nextflow_pipeline { test("-profile test") { then { - // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir($outputDir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_content: All files in ${params.outdir}/ with stable content + // stable_path: All files + folders in $outputDir/ with a stable path (including file name) + def stable_path = getAllFilesFromDir($outputDir, relative: true, includeDir: true) + // stable_content: All files in $outputDir/ with stable content def stable_content = getAllFilesFromDir($outputDir, ignoreFile: 'tests/.nftignore') assert workflow.success From 1d437120df169d28a33e175dcef75966b42e973f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Wed, 1 Jul 2026 15:34:14 +0200 Subject: [PATCH 027/102] Revert changes to default test to use params.outdir. --- tests/default.nf.test | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 3d5b36e..a8e2789 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -6,11 +6,17 @@ nextflow_pipeline { test("-profile test") { + when { + params { + outdir = "$outputDir" + } + } + then { - // stable_path: All files + folders in $outputDir/ with a stable path (including file name) - def stable_path = getAllFilesFromDir($outputDir, relative: true, includeDir: true) - // stable_content: All files in $outputDir/ with stable content - def stable_content = getAllFilesFromDir($outputDir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( From 43d01f5b92e8a100c73a812b39450c0a3e898014 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 12:07:00 +0200 Subject: [PATCH 028/102] Update test config to run in stub and remove unused arguments. --- conf/test.config | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/conf/test.config b/conf/test.config index 3d54b76..69aad4a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,12 +19,8 @@ process { } params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test to check if both pipelines are run sequentially' + config_profile_name = 'Test profile -stub' + config_profile_description = 'Minimal stub test to check that pipelines are run sequentially' - // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = '-profile test,docker' - oncoanalyser.params_file = '' - oncoanalyser.samplesheet = '' - oncoanalyser.additional_config = '' + oncoanalyser.nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } From d36495e901620f3735485bd8a30c660b6135dad9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 12:07:18 +0200 Subject: [PATCH 029/102] Fix indentation in test config --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 69aad4a..1be1059 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,5 +22,5 @@ params { config_profile_name = 'Test profile -stub' config_profile_description = 'Minimal stub test to check that pipelines are run sequentially' - oncoanalyser.nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' + oncoanalyser.nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } From ccd417c26d3b2a53a58db734ad95e5d628680b84 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 13:44:10 +0200 Subject: [PATCH 030/102] Ad publish block to main.nf --- main.nf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/main.nf b/main.nf index ecf1bcd..f7373b2 100644 --- a/main.nf +++ b/main.nf @@ -28,6 +28,8 @@ include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "./modules/local/nextflow/r workflow { + main: + NFCORE_ONCOANALYSER( 'nf-core/oncoanalyser', params.oncoanalyser.nextflow_opts, @@ -36,7 +38,14 @@ workflow { params.oncoanalyser.additional_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) + publish: + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output +} +output { + oncoanalyser_output { + path "oncoanalyser" + } } /* From a90a887d8835f9f885cbe5065649b62c9b8fab85 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 14:45:37 +0200 Subject: [PATCH 031/102] Update test name. --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index a8e2789..a60d2e2 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" - test("-profile test") { + test("-profile test (stub)") { when { params { From f9fa106c0813c0b0d379015589370d9202384669 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:18:24 +0200 Subject: [PATCH 032/102] Move code to worfklows/oncoflow.nf --- main.nf | 4 +--- workflows/oncoflow.nf | 13 ++++++++++++- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 0ed8cde..804267b 100644 --- a/main.nf +++ b/main.nf @@ -12,9 +12,7 @@ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "./modules/local/nextflow/run/main" - -include { ONCOFLOW } from './workflows/oncoflow' +include { ONCOFLOW } from './workflows/oncoflow' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_oncoflow_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_oncoflow_pipeline' /* diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 80e8f86..de73189 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -3,6 +3,7 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' /* @@ -20,6 +21,15 @@ workflow ONCOFLOW { def ch_versions = channel.empty() + NFCORE_ONCOANALYSER( + 'nf-core/oncoanalyser', + params.oncoanalyser.nextflow_opts, + params.oncoanalyser.params_file, + params.oncoanalyser.samplesheet, + params.oncoanalyser.additional_config, + workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), + ) + // // Collate and save software versions // @@ -49,7 +59,8 @@ workflow ONCOFLOW { newLine: true ) emit: - versions = ch_versions // channel: [ path(versions.yml) ] + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [ path(analysis_output_directory) ] + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 369f5c3c0d553fed80ce8f456b3475999c702574 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:20:50 +0200 Subject: [PATCH 033/102] Add publish block. --- main.nf | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 804267b..c5e2a91 100644 --- a/main.nf +++ b/main.nf @@ -61,8 +61,8 @@ workflow { // // WORKFLOW: Run main workflow // - CLINICALGENOMICS_ONCOFLOW ( - ) + CLINICALGENOMICS_ONCOFLOW () + // // SUBWORKFLOW: Run completion tasks // @@ -73,6 +73,15 @@ workflow { params.outdir, params.monochrome_logs, ) + + publish: + oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.oncoanalyser_output +} + +output { + oncoanalyser_output { + path "oncoanalyser" + } } /* From c7b450785b0293efa1f6856ab74a43c9660840c2 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:40:29 +0200 Subject: [PATCH 034/102] Fix bug in publish block. --- main.nf | 5 ++++- workflows/oncoflow.nf | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index c5e2a91..6611827 100644 --- a/main.nf +++ b/main.nf @@ -34,6 +34,9 @@ workflow CLINICALGENOMICS_ONCOFLOW { ONCOFLOW ( params.outdir, ) + + emit: + oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [ path(analysis_output_directory) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -75,7 +78,7 @@ workflow { ) publish: - oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.oncoanalyser_output + oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.out.oncoanalyser_output } output { diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index de73189..acb2d16 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -58,6 +58,7 @@ workflow ONCOFLOW { sort: true, newLine: true ) + emit: oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [ path(analysis_output_directory) ] versions = ch_versions // channel: [ path(versions.yml) ] From cff68d571118568005157519dd5cfbab4b0270a7 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:48:36 +0200 Subject: [PATCH 035/102] Change NEXTFLOW_RUN module test to run nf-core/demo in stub. --- modules/local/nextflow/run/tests/main.nf.test | 4 +- .../nextflow/run/tests/main.nf.test.snap | 87 +++---------------- 2 files changed, 14 insertions(+), 77 deletions(-) diff --git a/modules/local/nextflow/run/tests/main.nf.test b/modules/local/nextflow/run/tests/main.nf.test index 4c94b71..5380bb0 100644 --- a/modules/local/nextflow/run/tests/main.nf.test +++ b/modules/local/nextflow/run/tests/main.nf.test @@ -4,13 +4,13 @@ nextflow_process { script "modules/local/nextflow/run/main.nf" process "NEXTFLOW_RUN" - test("Nextflow run nf-core/demo - docker,test") { + test("Nextflow run nf-core/demo -revision 1.2.0 -profile docker,test -stub") { when { process { """ input[0] = 'nf-core/demo' - input[1] = '-ansi-log false -profile docker,test -revision 1.2.0' + input[1] = '-ansi-log false -profile docker,test -revision 1.2.0 -stub' input[2] = '' input[3] = '' input[4] = '' diff --git a/modules/local/nextflow/run/tests/main.nf.test.snap b/modules/local/nextflow/run/tests/main.nf.test.snap index 695fa29..13a0c8c 100644 --- a/modules/local/nextflow/run/tests/main.nf.test.snap +++ b/modules/local/nextflow/run/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Nextflow run nf-core/demo - docker,test": { + "Nextflow run nf-core/demo -revision 1.2.0 -profile docker,test -stub": { "content": [ { "COWPY": { @@ -21,14 +21,11 @@ "cowpy/cowpy.txt", "fastqc", "fastqc/SAMPLE1_PE", - "fastqc/SAMPLE1_PE/SAMPLE1_PE_1_fastqc.html", - "fastqc/SAMPLE1_PE/SAMPLE1_PE_2_fastqc.html", + "fastqc/SAMPLE1_PE/SAMPLE1_PE.html", "fastqc/SAMPLE2_PE", - "fastqc/SAMPLE2_PE/SAMPLE2_PE_1_fastqc.html", - "fastqc/SAMPLE2_PE/SAMPLE2_PE_2_fastqc.html", + "fastqc/SAMPLE2_PE/SAMPLE2_PE.html", "fastqc/SAMPLE3_SE", - "fastqc/SAMPLE3_SE/SAMPLE3_SE_1_fastqc.html", - "fastqc/SAMPLE3_SE/SAMPLE3_SE_2_fastqc.html", + "fastqc/SAMPLE3_SE/SAMPLE3_SE.html", "fq", "fq/SAMPLE1_PE", "fq/SAMPLE1_PE/SAMPLE1_PE_sample1_R1.fastq.gz", @@ -41,78 +38,18 @@ "fq/SAMPLE3_SE/SAMPLE3_SE_sample2_R1.fastq.gz", "multiqc", "multiqc/multiqc_data", - "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", - "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", - "multiqc/multiqc_data/llms-full.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc.parquet", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_fastqc.txt", - "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/.stub", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_demo_software_mqc_versions.yml" ], [ - "cowpy.txt:md5,9c8be9f4550989b40901f379cb1a605f", - "SAMPLE1_PE_1_fastqc.html:md5,b8f39b1132e08df4f7156b2f939a5ffd", - "SAMPLE1_PE_2_fastqc.html:md5,b446397d1660841c9ae419a56b68074b", - "SAMPLE2_PE_1_fastqc.html:md5,1fb86bc14c6c395a9f2a135cfd5e1960", - "SAMPLE2_PE_2_fastqc.html:md5,2bbe0772dd3d41edd53fe8a5ad00c952", - "SAMPLE3_SE_1_fastqc.html:md5,5c3c74d38ad82c233e8d810cdff63506", - "SAMPLE3_SE_2_fastqc.html:md5,c1071faf40a0769c0f91a5bf68d73296", + "cowpy.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAMPLE1_PE.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAMPLE2_PE.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAMPLE3_SE.html:md5,d41d8cd98f00b204e9800998ecf8427e", "SAMPLE1_PE_sample1_R1.fastq.gz:md5,7dd2fd0d542d9259d9aed53550907fae", "SAMPLE1_PE_sample1_R2.fastq.gz:md5,1995fe8488384d801807805f26ceca8a", "SAMPLE2_PE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e", @@ -121,10 +58,10 @@ "SAMPLE3_SE_sample2_R1.fastq.gz:md5,05dba9c26396cbdbe0e6da26f037106e" ] ], - "timestamp": "2026-06-29T12:24:29.271329", + "timestamp": "2026-07-02T17:47:51.590456", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.4" + "nextflow": "25.10.4" } } } \ No newline at end of file From c21e966d58e46060c16614c7143777cf05f4824c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:57:17 +0200 Subject: [PATCH 036/102] Update test config name and description. --- conf/test.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index 1be1059..e31fb65 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,8 +19,8 @@ process { } params { - config_profile_name = 'Test profile -stub' - config_profile_description = 'Minimal stub test to check that pipelines are run sequentially' + config_profile_name = 'Test profile (stub runs for all pipelines)' + config_profile_description = 'Minimal test where all pipelines are run in stub mode to check that pipelines are run sequentially' oncoanalyser.nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } From 05e9040bcdd1b370bca74cd95339690a621f6017 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 17:57:38 +0200 Subject: [PATCH 037/102] Update default test name. --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index a60d2e2..c3dd78c 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" - test("-profile test (stub)") { + test("-profile test (stub runs for all pipelines)") { when { params { From 738c7c3bb17c52d800841773dedf7faea62a0a63 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 2 Jul 2026 18:06:39 +0200 Subject: [PATCH 038/102] Update default test snapshot. --- tests/default.nf.test.snap | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 tests/default.nf.test.snap diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..feeb61f --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,22 @@ +{ + "-profile test (stub runs for all pipelines)": { + "content": [ + [ + "pipeline_info", + "pipeline_info/execution_report_2026-07-02_18-04-34.html", + "pipeline_info/execution_timeline_2026-07-02_18-04-34.html", + "pipeline_info/oncoflow_software_versions.yml", + "pipeline_info/params_2026-07-02_18-04-35.json", + "pipeline_info/pipeline_dag_2026-07-02_18-04-34.html" + ], + [ + + ] + ], + "timestamp": "2026-07-02T18:06:09.824955", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 7dbd93802db3d84c2b73495b2f6f0edeec8451a6 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:07:48 +0200 Subject: [PATCH 039/102] Restore test. --- tests/default.nf.test | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index c3dd78c..c4865df 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -14,13 +14,15 @@ nextflow_pipeline { then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/oncoflow_software_mqc_versions.yml"), // All stable path name, with a relative path stable_path, // All files with stable contents From 47f68d191606720b60e26807f020929ad8b9a1fe Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:07:56 +0200 Subject: [PATCH 040/102] Update snapshot. --- tests/default.nf.test.snap | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index feeb61f..f6e7c60 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,19 +1,16 @@ { "-profile test (stub runs for all pipelines)": { "content": [ + null, [ "pipeline_info", - "pipeline_info/execution_report_2026-07-02_18-04-34.html", - "pipeline_info/execution_timeline_2026-07-02_18-04-34.html", - "pipeline_info/oncoflow_software_versions.yml", - "pipeline_info/params_2026-07-02_18-04-35.json", - "pipeline_info/pipeline_dag_2026-07-02_18-04-34.html" + "pipeline_info/oncoflow_software_versions.yml" ], [ ] ], - "timestamp": "2026-07-02T18:06:09.824955", + "timestamp": "2026-07-03T10:06:07.707367", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From aa51fbc291095e3ad0e3de1a27094349a5c5869b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:19:58 +0200 Subject: [PATCH 041/102] style: NEXTFLOW_RUN. --- modules/local/nextflow/run/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index e33e5a0..fc9fe0c 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -12,7 +12,7 @@ process NEXTFLOW_RUN { val cache_dir // cache directory output: - path "results" , emit: output + path "results", emit: output val stdout, emit: log when: From 42d01eb60da1270ee546b0bb5890a64285df00f1 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:52:37 +0200 Subject: [PATCH 042/102] Update changelog. --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e8e704c..0d85987 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER`, using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. ### `Fixed` From c7342c567ad4aeda8e01c94655325ecc9559acb9 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Fri, 3 Jul 2026 10:56:56 +0200 Subject: [PATCH 043/102] style: modules/local/nextflow/run/main.nf --- modules/local/nextflow/run/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/nextflow/run/main.nf b/modules/local/nextflow/run/main.nf index e33e5a0..fc9fe0c 100644 --- a/modules/local/nextflow/run/main.nf +++ b/modules/local/nextflow/run/main.nf @@ -12,7 +12,7 @@ process NEXTFLOW_RUN { val cache_dir // cache directory output: - path "results" , emit: output + path "results", emit: output val stdout, emit: log when: From eaca0befc24a99311b975fbe0c47383ca4824c25 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:59:04 +0200 Subject: [PATCH 044/102] Update nftignore to also ignore `pipeline_info` files for all called pipelines. --- tests/.nftignore | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/.nftignore b/tests/.nftignore index 73eb92f..dc61148 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,2 +1,3 @@ .DS_Store pipeline_info/*.{html,json,txt,yml} +*/*/pipeline_info/*.{html,json,txt,yml} From 2d8c3db8e8ff9c193e3922e08d7972f0dc41ed71 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:59:30 +0200 Subject: [PATCH 045/102] Update default test to use ignore file. --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index c4865df..45fbbc8 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -14,7 +14,7 @@ nextflow_pipeline { then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore') // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') From 8679d89604ea2ecebe31636f81bf1ad3a1465603 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 10:59:38 +0200 Subject: [PATCH 046/102] Update snapshot. --- tests/default.nf.test.snap | 925 ++++++++++++++++++++++++++++++++++++- 1 file changed, 921 insertions(+), 4 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f6e7c60..50dde80 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -3,14 +3,931 @@ "content": [ null, [ - "pipeline_info", - "pipeline_info/oncoflow_software_versions.yml" + "oncoanalyser", + "oncoanalyser/results", + "oncoanalyser/results/pipeline_info", + "oncoanalyser/results/subject_a", + "oncoanalyser/results/subject_a/alignments", + "oncoanalyser/results/subject_a/alignments/dna", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.duplicate_freq.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.jitter_params.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.duplicate_freq.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.jitter_params.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam.bai", + "oncoanalyser/results/subject_a/amber", + "oncoanalyser/results/subject_a/amber/placeholder", + "oncoanalyser/results/subject_a/bamtools", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/chord", + "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv", + "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.prediction.tsv", + "oncoanalyser/results/subject_a/cider", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.locus_stats.tsv", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", + "oncoanalyser/results/subject_a/cobalt", + "oncoanalyser/results/subject_a/cobalt/placeholder", + "oncoanalyser/results/subject_a/cuppa", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.pred_summ.tsv", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.vis.png", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.vis_data.tsv", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", + "oncoanalyser/results/subject_a/esvee", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz.tbi", + "oncoanalyser/results/subject_a/isofox", + "oncoanalyser/results/subject_a/isofox/placeholder", + "oncoanalyser/results/subject_a/lilac", + "oncoanalyser/results/subject_a/lilac/placeholder", + "oncoanalyser/results/subject_a/linx", + "oncoanalyser/results/subject_a/linx/germline_annotations", + "oncoanalyser/results/subject_a/linx/germline_annotations/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_annotations", + "oncoanalyser/results/subject_a/linx/somatic_annotations/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_plots", + "oncoanalyser/results/subject_a/linx/somatic_plots/all", + "oncoanalyser/results/subject_a/linx/somatic_plots/all/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_plots/reportable", + "oncoanalyser/results/subject_a/linx/somatic_plots/reportable/placeholder", + "oncoanalyser/results/subject_a/linx/subject_a.tumor_linx.html", + "oncoanalyser/results/subject_a/logs", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.sh", + "oncoanalyser/results/subject_a/neo", + "oncoanalyser/results/subject_a/neo/annotated_fusions", + "oncoanalyser/results/subject_a/neo/annotated_fusions/subject_a.tumor.isf.neoepitope.tsv", + "oncoanalyser/results/subject_a/neo/finder", + "oncoanalyser/results/subject_a/neo/scorer", + "oncoanalyser/results/subject_a/orange", + "oncoanalyser/results/subject_a/orange/subject_a.tumor.orange.json", + "oncoanalyser/results/subject_a/orange/subject_a.tumor.orange.pdf", + "oncoanalyser/results/subject_a/pave", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/peach", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.events.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.gene.events.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.haplotypes.all.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.haplotypes.best.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.qc.tsv", + "oncoanalyser/results/subject_a/purple", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.cnv.gene.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.cnv.somatic.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.germline.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.somatic.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.purity.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.qc", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "oncoanalyser/results/subject_a/sage", + "oncoanalyser/results/subject_a/sage/germline", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage/somatic", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append", + "oncoanalyser/results/subject_a/sage_append/germline", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal_query.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_append/somatic", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor_query.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sigs", + "oncoanalyser/results/subject_a/sigs/placeholder", + "oncoanalyser/results/subject_a/teal", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.telbam.bam", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.telbam.bam.bai", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.{tellength.tsv}", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.telbam.bam", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.telbam.bam.bai", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.tellength.tsv", + "oncoanalyser/results/subject_a/virusbreakend", + "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.summary.tsv", + "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.virusbreakend.vcf", + "oncoanalyser/results/subject_a/virusinterpreter", + "oncoanalyser/results/subject_a/virusinterpreter/subject_a.tumor.virus.annotated.tsv", + "pipeline_info" ], [ - + "subject_a.normal.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.normal.ms_table.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.normal.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.ms_table.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.flag_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.frag_length.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.partition_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.flag_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.frag_length.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.partition_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.chord.mutation_contexts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.chord.prediction.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.cider.alignment_match.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.cider.layout.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.cider.vdj.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor_rna.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor_rna.cider.layout.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor_rna.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor_rna.cider.vdj.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.pred_summ.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.vis.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.vis_data.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.cuppa_data.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.esvee.germline.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.esvee.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.esvee.somatic.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.esvee.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.esvee.unfiltered.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.esvee.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_linx.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.amber.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.amber.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.amber.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.amber.command.run:md5,2836515da0462ecf3bd9853d9ad078af", + "subject_a.amber.command.sh:md5,ece04e00128d32c17f9348fe94e6f435", + "subject_a.chord.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.chord.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.chord.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.chord.command.run:md5,c0026a99ba89da86cf899f07d5f047da", + "subject_a.chord.command.sh:md5,9b71409e679713e28b017824bc25c0bc", + "subject_a.cobalt.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.cobalt.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.cobalt.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.cobalt.command.run:md5,f36ab620a124f79eb426c890544aeaf0", + "subject_a.cobalt.command.sh:md5,249ff2daaf99134cd74d36683d00e52b", + "subject_a.cuppa.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.cuppa.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.cuppa.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.cuppa.command.run:md5,39cd494902d7c7854b8572f41bd470d8", + "subject_a.cuppa.command.sh:md5,7bc0af7c494aa796a0eb34875c76d4f7", + "subject_a.esvee.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.esvee.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.esvee.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.esvee.command.run:md5,fa2e471b05e47b8e542196702c89d5cd", + "subject_a.esvee.command.sh:md5,3df68e38d29406d19e6dc0be882befd5", + "subject_a.isofox.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.isofox.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.isofox.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.isofox.command.run:md5,b7687c452c591e043d787464eb386794", + "subject_a.isofox.command.sh:md5,d8c9918ccfcfb4e26bcdded5466c7b14", + "subject_a.lilac.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.lilac.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.lilac.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.lilac.command.run:md5,8b094de64d4550077c1356f4c82032be", + "subject_a.lilac.command.sh:md5,067273b45d86fe02212dd41b074390b8", + "subject_a.linx_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.linx_germline.command.run:md5,049083495e5bbd80455f720a161c4699", + "subject_a.linx_germline.command.sh:md5,6810076ab4979a8a081283dea3ab65fa", + "subject_a.linx_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.linx_somatic.command.run:md5,6f514338f6fe9270111517156d48ca24", + "subject_a.linx_somatic.command.sh:md5,0be909d504771d4fb304bbc7680c2a00", + "subject_a.linx_visualiser.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_visualiser.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linx_visualiser.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.linx_visualiser.command.run:md5,587048087ac71608b3a4a8efba3e4de3", + "subject_a.linx_visualiser.command.sh:md5,b74ad1ea317fb89105326bd83666df3d", + "subject_a.linxreport.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linxreport.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.linxreport.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.linxreport.command.run:md5,9548322fc32718cf00a5925e7c45084a", + "subject_a.linxreport.command.sh:md5,82b46b4735acfc4a5f2777e0df80b183", + "subject_a.neo_annotate_fusions.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_annotate_fusions.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_annotate_fusions.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.neo_annotate_fusions.command.run:md5,372766806db1c1b3eed83d4113654e4a", + "subject_a.neo_annotate_fusions.command.sh:md5,fc40ed44ab1936fea00a7a376ba6ed97", + "subject_a.neo_finder.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_finder.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_finder.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.neo_finder.command.run:md5,b14264f9336bcba30146aa9bb5a10b08", + "subject_a.neo_finder.command.sh:md5,d4d1109852cb5ffbc7d1dc5e312f3d98", + "subject_a.neo_scorer.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_scorer.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.neo_scorer.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.neo_scorer.command.run:md5,56f9d505639565abb2362b1d2cd54f29", + "subject_a.neo_scorer.command.sh:md5,072139d9fcee64b2638c13f0017c4fc7", + "subject_a.orange.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.orange.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.orange.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.orange.command.run:md5,12a115ccc9d9cdff6b1926710f2aef7e", + "subject_a.orange.command.sh:md5,939b1e1525c1aa3b5d7f75cc3b217f0e", + "subject_a.pave_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.pave_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.pave_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.pave_germline.command.run:md5,e336a4fdd8c22f3325cff9b6e57f255c", + "subject_a.pave_germline.command.sh:md5,343f61725ed8aca93842f860f40acffa", + "subject_a.pave_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.pave_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.pave_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.pave_somatic.command.run:md5,3ddfc46c05ed671709500410164da361", + "subject_a.pave_somatic.command.sh:md5,c3d4bc9ec34f6e33b3fe7f6fd7b00c3f", + "subject_a.peach.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.peach.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.peach.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.peach.command.run:md5,fa5bd1b2c05871807c4889246c61bb75", + "subject_a.peach.command.sh:md5,28b75a36763d0772d9d038c925aa569b", + "subject_a.purple.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.purple.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.purple.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.purple.command.run:md5,d5bce809c62f4125112798f7df025cea", + "subject_a.purple.command.sh:md5,00f71a94eb7d3d3b4568db8abc522b5a", + "subject_a.sage_append_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_append_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_append_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.sage_append_germline.command.run:md5,9cfa7464b2d092af3849af8e1157de7b", + "subject_a.sage_append_germline.command.sh:md5,b56a330cd442cae80fddf67e41b8e2e6", + "subject_a.sage_append_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_append_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_append_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.sage_append_somatic.command.run:md5,52109d9732fbf77afab80a6cbdb00ccd", + "subject_a.sage_append_somatic.command.sh:md5,fbc57d331e476b200e34afd53ef1e40a", + "subject_a.sage_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.sage_germline.command.run:md5,19b11d861f4496e79e632d17649eef66", + "subject_a.sage_germline.command.sh:md5,8a36236f7235dd2f852d280fc8e96b78", + "subject_a.sage_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sage_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.sage_somatic.command.run:md5,8d79acc7a9c20d6db1b8b83e2d9975b4", + "subject_a.sage_somatic.command.sh:md5,b49e27b48f909890e9b94016e1f38caf", + "subject_a.sigs.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sigs.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.sigs.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.sigs.command.run:md5,bab0407bbcc04f6e4b3f4faf19035800", + "subject_a.sigs.command.sh:md5,6008af259edb80b5fd5b966e35f69dc5", + "subject_a.teal_pipeline.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.teal_pipeline.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.teal_pipeline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.teal_pipeline.command.run:md5,0119e9ccd5b60d49a65c11a8dd839671", + "subject_a.teal_pipeline.command.sh:md5,6d050b9ecdc8f3e5568c54548a609e97", + "subject_a.teal_prep.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.teal_prep.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.teal_prep.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.teal_prep.command.run:md5,cca855e3580cc9d6ddb9b8d7af98fa8b", + "subject_a.teal_prep.command.sh:md5,cc5e17ec71fe1a5d768c71862ad95ec5", + "subject_a.virusbreakend.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.virusbreakend.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.virusbreakend.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.virusbreakend.command.run:md5,79054f9bc1ffb521a47c425257d638ff", + "subject_a.virusbreakend.command.sh:md5,38c53328ed48069a23b3855f325901c7", + "subject_a.virusinterpreter.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.virusinterpreter.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a.virusinterpreter.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.virusinterpreter.command.run:md5,ddf25c3dca68c270e2d710b3415adb8c", + "subject_a.virusinterpreter.command.sh:md5,5ad3b725b50b0f8237c6a4ba3a991570", + "subject_a_subject_a.normal.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.normal.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.normal.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.normal.bamtools.command.run:md5,5bf3a1fafaf64c1a4a454ffe5118bd95", + "subject_a_subject_a.normal.bamtools.command.sh:md5,497cf77f9778b9cf5cb4204c06a8860c", + "subject_a_subject_a.normal.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.normal.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.normal.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.normal.redux.command.run:md5,ff509f7539fb9d44b523a2b2841660e5", + "subject_a_subject_a.normal.redux.command.sh:md5,73bcabd515e72b50c9e05624da40c60b", + "subject_a_subject_a.tumor.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.tumor.bamtools.command.run:md5,77bf3a006e088114b8ce7e916b909e30", + "subject_a_subject_a.tumor.bamtools.command.sh:md5,442b1e6b1e6a9dbe32326197ec8253bf", + "subject_a_subject_a.tumor.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.tumor.cider.command.run:md5,65f1e17c12c9c794b22aee6adc1b7f58", + "subject_a_subject_a.tumor.cider.command.sh:md5,80c5fda774fa9fb3ee613cd613f4ee00", + "subject_a_subject_a.tumor.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.tumor.redux.command.run:md5,ee1103e07c65bfa38a72b87615017ba3", + "subject_a_subject_a.tumor.redux.command.sh:md5,f9324772e908bfdc70079a1aaf1680f4", + "subject_a_subject_a.tumor_rna.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor_rna.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", + "subject_a_subject_a.tumor_rna.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_subject_a.tumor_rna.cider.command.run:md5,76f67680df6d2396427ee71620bf505b", + "subject_a_subject_a.tumor_rna.cider.command.sh:md5,d4e8146a5505ec387fcd591db4d2d56a", + "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.orange.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.pave.germline.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.pave.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.pave.somatic.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.pave.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.gene.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.haplotypes.all.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.haplotypes.best.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.qc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.cnv.gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.cnv.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.driver.catalog.germline.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.driver.catalog.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.purple.germline.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.purple.purity.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.qc:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.purple.somatic.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.purple.sv.germline.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.purple.sv.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.normal.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.sage.germline.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.sage.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.sage.somatic.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.sage.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.normal.frag_lengths.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.normal.sage.append.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.frag_lengths.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.sage.append.vcf.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.{tellength.tsv}:md5,d41d8cd98f00b204e9800998ecf8427e", + { + "absolute": true, + "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", + "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", + "directory": false, + "file": true, + "freeSpace": 262021586944, + "hidden": false, + "name": "subject_a.tumor.teal.breakend.tsv.gz", + "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal", + "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", + "totalSpace": 994662584320, + "usableSpace": 262021586944 + }, + "subject_a.tumor.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-03T10:06:07.707367", + "timestamp": "2026-07-03T10:56:34.290551", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 66eb6ff7acbc6c9dc690078932a9693334e13cb5 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 11:02:20 +0200 Subject: [PATCH 047/102] Update changelog. --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d85987..d576083 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,9 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Fixed` +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to always use the `.nftignore` file when collecting files/directories. + ### `Dependencies` ### `Deprecated` From d9b6e93d2bf58b68664d11779b37ec947d4f1568 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:04:27 +0200 Subject: [PATCH 048/102] Update .nftignore to ignore pipeline_info, multiqc and vep files for all run pipelines. --- tests/.nftignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/.nftignore b/tests/.nftignore index dc61148..3224e59 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,3 +1,5 @@ .DS_Store pipeline_info/*.{html,json,txt,yml} -*/*/pipeline_info/*.{html,json,txt,yml} +**/pipeline_info/*.{html,json,txt,yml} +**/multiqc/** +**/vep/*.{html} From 45ef5a4df018283e007c5ce75d7dfbafb7cbb546 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:04:33 +0200 Subject: [PATCH 049/102] Update default test to not capture `pipeline_info` files for run pipelines. --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 45fbbc8..ae0c517 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -14,7 +14,7 @@ nextflow_pipeline { then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', '**/pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') From cc769a4f35c8358cec3101472505eca261a22654 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:05:42 +0200 Subject: [PATCH 050/102] Update changelog. --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d576083..74c8f3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,8 +14,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Fixed` -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info` files for all pipelines. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to always use the `.nftignore` file when collecting files/directories. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info`, `multiqc`, and `vep` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for run pipelines. ### `Dependencies` From a3d94be5b8ff9508cd80e40329e66efd546098fc Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:06:58 +0200 Subject: [PATCH 051/102] Update changelog. --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74c8f3b..f0bbef7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER`, using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. ### `Fixed` From 7152e7ab188624ca9a0b0ff79cc55d9aac20bf1e Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:09:19 +0200 Subject: [PATCH 052/102] Add `Changed` header to changelog. Move relevant entries there. --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f0bbef7..e45ca14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,11 +12,13 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. -### `Fixed` +### `Changed` - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info`, `multiqc`, and `vep` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for run pipelines. +### `Fixed` + ### `Dependencies` ### `Deprecated` From eb77d3432da6438bc8853657c91831a526ee3921 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:09:24 +0200 Subject: [PATCH 053/102] Update snapshot. --- tests/default.nf.test.snap | 174 +++++++++++++++++++------------------ 1 file changed, 88 insertions(+), 86 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 50dde80..3b5318f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -6,6 +6,7 @@ "oncoanalyser", "oncoanalyser/results", "oncoanalyser/results/pipeline_info", + "oncoanalyser/results/pipeline_info/software_versions.yml", "oncoanalyser/results/subject_a", "oncoanalyser/results/subject_a/alignments", "oncoanalyser/results/subject_a/alignments/dna", @@ -321,7 +322,8 @@ "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.virusbreakend.vcf", "oncoanalyser/results/subject_a/virusinterpreter", "oncoanalyser/results/subject_a/virusinterpreter/subject_a.tumor.virus.annotated.tsv", - "pipeline_info" + "pipeline_info", + "pipeline_info/oncoflow_software_versions.yml" ], [ "subject_a.normal.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -332,13 +334,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.normal.ms_table.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.normal.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -350,13 +352,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.ms_table.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -379,13 +381,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.cider.alignment_match.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -394,13 +396,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.cider.layout.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -409,13 +411,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.cider.vdj.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, { "absolute": true, @@ -423,13 +425,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor_rna.cider.alignment_match.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor_rna.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -438,13 +440,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor_rna.cider.layout.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor_rna.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -453,13 +455,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor_rna.cider.vdj.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.cuppa.pred_summ.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -471,13 +473,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.cuppa_data.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, { "absolute": true, @@ -485,13 +487,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.esvee.germline.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.esvee.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -500,13 +502,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.esvee.somatic.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.esvee.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -515,13 +517,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.esvee.unfiltered.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.esvee.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -534,172 +536,172 @@ "subject_a.amber.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.amber.command.run:md5,2836515da0462ecf3bd9853d9ad078af", + "subject_a.amber.command.run:md5,7c5f085daaffdb13bbe5b6c56b0c11a4", "subject_a.amber.command.sh:md5,ece04e00128d32c17f9348fe94e6f435", "subject_a.chord.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.chord.command.run:md5,c0026a99ba89da86cf899f07d5f047da", + "subject_a.chord.command.run:md5,05b32754c6c854fc0f4258ee29e77737", "subject_a.chord.command.sh:md5,9b71409e679713e28b017824bc25c0bc", "subject_a.cobalt.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cobalt.command.run:md5,f36ab620a124f79eb426c890544aeaf0", + "subject_a.cobalt.command.run:md5,59323817bed967c5e0d42de80fbe5509", "subject_a.cobalt.command.sh:md5,249ff2daaf99134cd74d36683d00e52b", "subject_a.cuppa.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cuppa.command.run:md5,39cd494902d7c7854b8572f41bd470d8", + "subject_a.cuppa.command.run:md5,dfdbe67d70fb8ab337a3fabc219c2f94", "subject_a.cuppa.command.sh:md5,7bc0af7c494aa796a0eb34875c76d4f7", "subject_a.esvee.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.esvee.command.run:md5,fa2e471b05e47b8e542196702c89d5cd", + "subject_a.esvee.command.run:md5,15ac9cc6681a81ed85a3cf18f6276839", "subject_a.esvee.command.sh:md5,3df68e38d29406d19e6dc0be882befd5", "subject_a.isofox.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.isofox.command.run:md5,b7687c452c591e043d787464eb386794", + "subject_a.isofox.command.run:md5,55c75581a399167e91e4ca316d9075a2", "subject_a.isofox.command.sh:md5,d8c9918ccfcfb4e26bcdded5466c7b14", "subject_a.lilac.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.lilac.command.run:md5,8b094de64d4550077c1356f4c82032be", + "subject_a.lilac.command.run:md5,c528fd7d0be34c94bce4733dcc76c75e", "subject_a.lilac.command.sh:md5,067273b45d86fe02212dd41b074390b8", "subject_a.linx_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_germline.command.run:md5,049083495e5bbd80455f720a161c4699", + "subject_a.linx_germline.command.run:md5,1260a758b2d82b3f25a9c65cef3d59dc", "subject_a.linx_germline.command.sh:md5,6810076ab4979a8a081283dea3ab65fa", "subject_a.linx_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_somatic.command.run:md5,6f514338f6fe9270111517156d48ca24", + "subject_a.linx_somatic.command.run:md5,4c725f99e154dced9ceb92c55d957a65", "subject_a.linx_somatic.command.sh:md5,0be909d504771d4fb304bbc7680c2a00", "subject_a.linx_visualiser.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_visualiser.command.run:md5,587048087ac71608b3a4a8efba3e4de3", + "subject_a.linx_visualiser.command.run:md5,dd59bac169be5a8309107592024013ef", "subject_a.linx_visualiser.command.sh:md5,b74ad1ea317fb89105326bd83666df3d", "subject_a.linxreport.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linxreport.command.run:md5,9548322fc32718cf00a5925e7c45084a", + "subject_a.linxreport.command.run:md5,920df0eb6edfbd23250f785bc4cc31b1", "subject_a.linxreport.command.sh:md5,82b46b4735acfc4a5f2777e0df80b183", "subject_a.neo_annotate_fusions.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_annotate_fusions.command.run:md5,372766806db1c1b3eed83d4113654e4a", + "subject_a.neo_annotate_fusions.command.run:md5,1986396373be4b686fd7d00709844fec", "subject_a.neo_annotate_fusions.command.sh:md5,fc40ed44ab1936fea00a7a376ba6ed97", "subject_a.neo_finder.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_finder.command.run:md5,b14264f9336bcba30146aa9bb5a10b08", + "subject_a.neo_finder.command.run:md5,da233a2b7ec61e3068fb0a1c203047ea", "subject_a.neo_finder.command.sh:md5,d4d1109852cb5ffbc7d1dc5e312f3d98", "subject_a.neo_scorer.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_scorer.command.run:md5,56f9d505639565abb2362b1d2cd54f29", + "subject_a.neo_scorer.command.run:md5,de7054d2dddff718afa33d5f1a47d70f", "subject_a.neo_scorer.command.sh:md5,072139d9fcee64b2638c13f0017c4fc7", "subject_a.orange.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.orange.command.run:md5,12a115ccc9d9cdff6b1926710f2aef7e", + "subject_a.orange.command.run:md5,5707fd73fa4ee9465fe6c244673acc35", "subject_a.orange.command.sh:md5,939b1e1525c1aa3b5d7f75cc3b217f0e", "subject_a.pave_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_germline.command.run:md5,e336a4fdd8c22f3325cff9b6e57f255c", + "subject_a.pave_germline.command.run:md5,12c7431c7953f018d0d9a797ac63edba", "subject_a.pave_germline.command.sh:md5,343f61725ed8aca93842f860f40acffa", "subject_a.pave_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_somatic.command.run:md5,3ddfc46c05ed671709500410164da361", + "subject_a.pave_somatic.command.run:md5,4619bd98550242fd39a0e9ff060c8bdf", "subject_a.pave_somatic.command.sh:md5,c3d4bc9ec34f6e33b3fe7f6fd7b00c3f", "subject_a.peach.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.peach.command.run:md5,fa5bd1b2c05871807c4889246c61bb75", + "subject_a.peach.command.run:md5,c4252f68810c06df770b17dafcb060e2", "subject_a.peach.command.sh:md5,28b75a36763d0772d9d038c925aa569b", "subject_a.purple.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.purple.command.run:md5,d5bce809c62f4125112798f7df025cea", + "subject_a.purple.command.run:md5,a334badd897e07f70ca305d991dddd13", "subject_a.purple.command.sh:md5,00f71a94eb7d3d3b4568db8abc522b5a", "subject_a.sage_append_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_germline.command.run:md5,9cfa7464b2d092af3849af8e1157de7b", + "subject_a.sage_append_germline.command.run:md5,fe0fbe8f59ee392e96c3d2e2ba5b6133", "subject_a.sage_append_germline.command.sh:md5,b56a330cd442cae80fddf67e41b8e2e6", "subject_a.sage_append_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_somatic.command.run:md5,52109d9732fbf77afab80a6cbdb00ccd", + "subject_a.sage_append_somatic.command.run:md5,0437fd1130c55ce02da6afe369f71cdf", "subject_a.sage_append_somatic.command.sh:md5,fbc57d331e476b200e34afd53ef1e40a", "subject_a.sage_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_germline.command.run:md5,19b11d861f4496e79e632d17649eef66", + "subject_a.sage_germline.command.run:md5,e4e7d512e4738d08fec8d48de404d9f1", "subject_a.sage_germline.command.sh:md5,8a36236f7235dd2f852d280fc8e96b78", "subject_a.sage_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_somatic.command.run:md5,8d79acc7a9c20d6db1b8b83e2d9975b4", + "subject_a.sage_somatic.command.run:md5,5f36d859bc795cd83686aa1d0c4cbcde", "subject_a.sage_somatic.command.sh:md5,b49e27b48f909890e9b94016e1f38caf", "subject_a.sigs.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sigs.command.run:md5,bab0407bbcc04f6e4b3f4faf19035800", + "subject_a.sigs.command.run:md5,6cf23e80c832993bd48a95768629b8e9", "subject_a.sigs.command.sh:md5,6008af259edb80b5fd5b966e35f69dc5", "subject_a.teal_pipeline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_pipeline.command.run:md5,0119e9ccd5b60d49a65c11a8dd839671", + "subject_a.teal_pipeline.command.run:md5,f16050d314758e6bb571561c7c090b94", "subject_a.teal_pipeline.command.sh:md5,6d050b9ecdc8f3e5568c54548a609e97", "subject_a.teal_prep.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_prep.command.run:md5,cca855e3580cc9d6ddb9b8d7af98fa8b", + "subject_a.teal_prep.command.run:md5,f5f4ce4092c55ab8d163d76a5321716a", "subject_a.teal_prep.command.sh:md5,cc5e17ec71fe1a5d768c71862ad95ec5", "subject_a.virusbreakend.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusbreakend.command.run:md5,79054f9bc1ffb521a47c425257d638ff", + "subject_a.virusbreakend.command.run:md5,a80b148c5860d00790afc67483c18c1f", "subject_a.virusbreakend.command.sh:md5,38c53328ed48069a23b3855f325901c7", "subject_a.virusinterpreter.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusinterpreter.command.run:md5,ddf25c3dca68c270e2d710b3415adb8c", + "subject_a.virusinterpreter.command.run:md5,51b7dee9faa095427a62322b623ea450", "subject_a.virusinterpreter.command.sh:md5,5ad3b725b50b0f8237c6a4ba3a991570", "subject_a_subject_a.normal.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.bamtools.command.run:md5,5bf3a1fafaf64c1a4a454ffe5118bd95", + "subject_a_subject_a.normal.bamtools.command.run:md5,2282059872d78fcb96be2081a17a0104", "subject_a_subject_a.normal.bamtools.command.sh:md5,497cf77f9778b9cf5cb4204c06a8860c", "subject_a_subject_a.normal.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.redux.command.run:md5,ff509f7539fb9d44b523a2b2841660e5", + "subject_a_subject_a.normal.redux.command.run:md5,171ef8b80e2ce3121f7177dfd62f0b00", "subject_a_subject_a.normal.redux.command.sh:md5,73bcabd515e72b50c9e05624da40c60b", "subject_a_subject_a.tumor.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.bamtools.command.run:md5,77bf3a006e088114b8ce7e916b909e30", + "subject_a_subject_a.tumor.bamtools.command.run:md5,48b2d08804c391cae4dcfdaec1705ab9", "subject_a_subject_a.tumor.bamtools.command.sh:md5,442b1e6b1e6a9dbe32326197ec8253bf", "subject_a_subject_a.tumor.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.cider.command.run:md5,65f1e17c12c9c794b22aee6adc1b7f58", + "subject_a_subject_a.tumor.cider.command.run:md5,5251254ccb8e2d4baf58d0a6b1cbaa5d", "subject_a_subject_a.tumor.cider.command.sh:md5,80c5fda774fa9fb3ee613cd613f4ee00", "subject_a_subject_a.tumor.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.redux.command.run:md5,ee1103e07c65bfa38a72b87615017ba3", + "subject_a_subject_a.tumor.redux.command.run:md5,149f26486ed09e7ab6e688d74a0cc7c8", "subject_a_subject_a.tumor.redux.command.sh:md5,f9324772e908bfdc70079a1aaf1680f4", "subject_a_subject_a.tumor_rna.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor_rna.cider.command.run:md5,76f67680df6d2396427ee71620bf505b", + "subject_a_subject_a.tumor_rna.cider.command.run:md5,7d678cefb25eb7236e0237694a0ce134", "subject_a_subject_a.tumor_rna.cider.command.sh:md5,d4e8146a5505ec387fcd591db4d2d56a", "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -710,13 +712,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.pave.germline.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.pave.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -725,13 +727,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.pave.somatic.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.pave.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.peach.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -749,13 +751,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.purple.germline.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, "subject_a.tumor.purple.purity.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.qc:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -765,13 +767,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.purple.somatic.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, { "absolute": true, @@ -779,13 +781,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593808384, "hidden": false, "name": "subject_a.tumor.purple.sv.germline.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593808384 }, { "absolute": true, @@ -793,13 +795,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593804288, "hidden": false, "name": "subject_a.tumor.purple.sv.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593804288 }, "subject_a.normal.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -812,13 +814,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.tumor.sage.germline.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, "subject_a.tumor.sage.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -832,13 +834,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.tumor.sage.somatic.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, "subject_a.tumor.sage.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", { @@ -847,13 +849,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.normal.frag_lengths.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, { "absolute": true, @@ -861,13 +863,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.normal.sage.append.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -877,13 +879,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.tumor.frag_lengths.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, { "absolute": true, @@ -891,13 +893,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.tumor.sage.append.vcf.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -911,13 +913,13 @@ "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", "directory": false, "file": true, - "freeSpace": 262021586944, + "freeSpace": 258593792000, "hidden": false, "name": "subject_a.tumor.teal.breakend.tsv.gz", "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal", "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", "totalSpace": 994662584320, - "usableSpace": 262021586944 + "usableSpace": 258593792000 }, "subject_a.tumor.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -927,7 +929,7 @@ "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-03T10:56:34.290551", + "timestamp": "2026-07-03T12:07:29.966578", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From db3cc04d318b0fe45ee8b3756352c23bcd73c273 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 3 Jul 2026 12:11:50 +0200 Subject: [PATCH 054/102] Remove vep files from nftignore --- CHANGELOG.md | 2 +- tests/.nftignore | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e45ca14..6af19ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Changed` -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info`, `multiqc`, and `vep` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for run pipelines. ### `Fixed` diff --git a/tests/.nftignore b/tests/.nftignore index 3224e59..3e6982a 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -2,4 +2,3 @@ pipeline_info/*.{html,json,txt,yml} **/pipeline_info/*.{html,json,txt,yml} **/multiqc/** -**/vep/*.{html} From 72441584268f2db7a3d9d58cda51bb8c5cebe2fd Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 09:58:22 +0200 Subject: [PATCH 055/102] Update nftignore to ignore gzipped files from oncoanalyser. --- tests/.nftignore | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/.nftignore b/tests/.nftignore index 3e6982a..7dd0c11 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -2,3 +2,4 @@ pipeline_info/*.{html,json,txt,yml} **/pipeline_info/*.{html,json,txt,yml} **/multiqc/** +oncoanalyser/**/*.gz From 4b0c987af74a32f31da5abed373fe6dc326315d9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 09:58:27 +0200 Subject: [PATCH 056/102] Update snapshot. --- tests/default.nf.test.snap | 420 ++++--------------------------------- 1 file changed, 35 insertions(+), 385 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3b5318f..0ff16e4 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -328,38 +328,10 @@ [ "subject_a.normal.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.normal.ms_table.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.normal.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.ms_table.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -375,156 +347,16 @@ "subject_a.tumor.bam_metric.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.chord.mutation_contexts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.chord.prediction.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.cider.alignment_match.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.cider.layout.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.cider.vdj.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor_rna.cider.alignment_match.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor_rna.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor_rna.cider.layout.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor_rna.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor_rna.cider.vdj.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.cuppa.pred_summ.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.cuppa.vis.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.cuppa.vis_data.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.cuppa_data.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.esvee.germline.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.esvee.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.esvee.somatic.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.esvee.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.esvee.unfiltered.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.esvee.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -536,205 +368,177 @@ "subject_a.amber.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.amber.command.run:md5,7c5f085daaffdb13bbe5b6c56b0c11a4", + "subject_a.amber.command.run:md5,fc9d0a570871e2bb82ada7fe5109ed76", "subject_a.amber.command.sh:md5,ece04e00128d32c17f9348fe94e6f435", "subject_a.chord.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.chord.command.run:md5,05b32754c6c854fc0f4258ee29e77737", + "subject_a.chord.command.run:md5,f7d8e437697e63f48733dc77331b30bd", "subject_a.chord.command.sh:md5,9b71409e679713e28b017824bc25c0bc", "subject_a.cobalt.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cobalt.command.run:md5,59323817bed967c5e0d42de80fbe5509", + "subject_a.cobalt.command.run:md5,398ed5c2839a9ce225afe15f03795037", "subject_a.cobalt.command.sh:md5,249ff2daaf99134cd74d36683d00e52b", "subject_a.cuppa.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cuppa.command.run:md5,dfdbe67d70fb8ab337a3fabc219c2f94", + "subject_a.cuppa.command.run:md5,e9e1b457f4fdfe0fe8691ae6b3552738", "subject_a.cuppa.command.sh:md5,7bc0af7c494aa796a0eb34875c76d4f7", "subject_a.esvee.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.esvee.command.run:md5,15ac9cc6681a81ed85a3cf18f6276839", + "subject_a.esvee.command.run:md5,d8c3bf6adb24e390cb5ce819376465a0", "subject_a.esvee.command.sh:md5,3df68e38d29406d19e6dc0be882befd5", "subject_a.isofox.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.isofox.command.run:md5,55c75581a399167e91e4ca316d9075a2", + "subject_a.isofox.command.run:md5,78691a7d9b5874b2a96d97824f76c1fc", "subject_a.isofox.command.sh:md5,d8c9918ccfcfb4e26bcdded5466c7b14", "subject_a.lilac.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.lilac.command.run:md5,c528fd7d0be34c94bce4733dcc76c75e", + "subject_a.lilac.command.run:md5,64c8db04b7af589b3e3a64735a0a91b4", "subject_a.lilac.command.sh:md5,067273b45d86fe02212dd41b074390b8", "subject_a.linx_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_germline.command.run:md5,1260a758b2d82b3f25a9c65cef3d59dc", + "subject_a.linx_germline.command.run:md5,91a0120ca2f85f79582430dd30f633ff", "subject_a.linx_germline.command.sh:md5,6810076ab4979a8a081283dea3ab65fa", "subject_a.linx_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_somatic.command.run:md5,4c725f99e154dced9ceb92c55d957a65", + "subject_a.linx_somatic.command.run:md5,d8de346206907980310c5ae3078e290b", "subject_a.linx_somatic.command.sh:md5,0be909d504771d4fb304bbc7680c2a00", "subject_a.linx_visualiser.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_visualiser.command.run:md5,dd59bac169be5a8309107592024013ef", + "subject_a.linx_visualiser.command.run:md5,a1ad8de9ae1827b703c29b6ed5b3f137", "subject_a.linx_visualiser.command.sh:md5,b74ad1ea317fb89105326bd83666df3d", "subject_a.linxreport.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linxreport.command.run:md5,920df0eb6edfbd23250f785bc4cc31b1", + "subject_a.linxreport.command.run:md5,bfb1f0210852ada894b4e2378495c25d", "subject_a.linxreport.command.sh:md5,82b46b4735acfc4a5f2777e0df80b183", "subject_a.neo_annotate_fusions.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_annotate_fusions.command.run:md5,1986396373be4b686fd7d00709844fec", + "subject_a.neo_annotate_fusions.command.run:md5,6cceda3a4623f2448c8c6e09bc22a54b", "subject_a.neo_annotate_fusions.command.sh:md5,fc40ed44ab1936fea00a7a376ba6ed97", "subject_a.neo_finder.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_finder.command.run:md5,da233a2b7ec61e3068fb0a1c203047ea", + "subject_a.neo_finder.command.run:md5,b01e194ebdae2bb5b39af6500633dd77", "subject_a.neo_finder.command.sh:md5,d4d1109852cb5ffbc7d1dc5e312f3d98", "subject_a.neo_scorer.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_scorer.command.run:md5,de7054d2dddff718afa33d5f1a47d70f", + "subject_a.neo_scorer.command.run:md5,8bc4c25d0ef4634407fcf9dff4261e37", "subject_a.neo_scorer.command.sh:md5,072139d9fcee64b2638c13f0017c4fc7", "subject_a.orange.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.orange.command.run:md5,5707fd73fa4ee9465fe6c244673acc35", + "subject_a.orange.command.run:md5,33bd5c6c7dae6e4c176ab081dc0459bd", "subject_a.orange.command.sh:md5,939b1e1525c1aa3b5d7f75cc3b217f0e", "subject_a.pave_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_germline.command.run:md5,12c7431c7953f018d0d9a797ac63edba", + "subject_a.pave_germline.command.run:md5,ed973db670b2313e67653637dbca2db1", "subject_a.pave_germline.command.sh:md5,343f61725ed8aca93842f860f40acffa", "subject_a.pave_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_somatic.command.run:md5,4619bd98550242fd39a0e9ff060c8bdf", + "subject_a.pave_somatic.command.run:md5,ce1f736b2b41002035f8a6264b8cbbb6", "subject_a.pave_somatic.command.sh:md5,c3d4bc9ec34f6e33b3fe7f6fd7b00c3f", "subject_a.peach.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.peach.command.run:md5,c4252f68810c06df770b17dafcb060e2", + "subject_a.peach.command.run:md5,df2d1b71f1b523d5beb1762568568df8", "subject_a.peach.command.sh:md5,28b75a36763d0772d9d038c925aa569b", "subject_a.purple.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.purple.command.run:md5,a334badd897e07f70ca305d991dddd13", + "subject_a.purple.command.run:md5,6b31d72e7e56c771b054d1d29c458965", "subject_a.purple.command.sh:md5,00f71a94eb7d3d3b4568db8abc522b5a", "subject_a.sage_append_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_germline.command.run:md5,fe0fbe8f59ee392e96c3d2e2ba5b6133", + "subject_a.sage_append_germline.command.run:md5,52425702cc3ffc22fc20182b361ebb6e", "subject_a.sage_append_germline.command.sh:md5,b56a330cd442cae80fddf67e41b8e2e6", "subject_a.sage_append_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_somatic.command.run:md5,0437fd1130c55ce02da6afe369f71cdf", + "subject_a.sage_append_somatic.command.run:md5,99f50da5a9774a9926f710b6e3fe4c37", "subject_a.sage_append_somatic.command.sh:md5,fbc57d331e476b200e34afd53ef1e40a", "subject_a.sage_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_germline.command.run:md5,e4e7d512e4738d08fec8d48de404d9f1", + "subject_a.sage_germline.command.run:md5,7e8f4fb054ce4a014382a055792a95e0", "subject_a.sage_germline.command.sh:md5,8a36236f7235dd2f852d280fc8e96b78", "subject_a.sage_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_somatic.command.run:md5,5f36d859bc795cd83686aa1d0c4cbcde", + "subject_a.sage_somatic.command.run:md5,c49f6502e2f6893878eeb16a41227b23", "subject_a.sage_somatic.command.sh:md5,b49e27b48f909890e9b94016e1f38caf", "subject_a.sigs.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sigs.command.run:md5,6cf23e80c832993bd48a95768629b8e9", + "subject_a.sigs.command.run:md5,cf307f3570167466b7f5d20da28d7e93", "subject_a.sigs.command.sh:md5,6008af259edb80b5fd5b966e35f69dc5", "subject_a.teal_pipeline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_pipeline.command.run:md5,f16050d314758e6bb571561c7c090b94", + "subject_a.teal_pipeline.command.run:md5,cb35186b76e6ece19c8f2516afc1e58e", "subject_a.teal_pipeline.command.sh:md5,6d050b9ecdc8f3e5568c54548a609e97", "subject_a.teal_prep.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_prep.command.run:md5,f5f4ce4092c55ab8d163d76a5321716a", + "subject_a.teal_prep.command.run:md5,6e45bb5ddd579542fc47e7c6f04891e0", "subject_a.teal_prep.command.sh:md5,cc5e17ec71fe1a5d768c71862ad95ec5", "subject_a.virusbreakend.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusbreakend.command.run:md5,a80b148c5860d00790afc67483c18c1f", + "subject_a.virusbreakend.command.run:md5,5e2505af840239aeefd0dbc77f3ad74f", "subject_a.virusbreakend.command.sh:md5,38c53328ed48069a23b3855f325901c7", "subject_a.virusinterpreter.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusinterpreter.command.run:md5,51b7dee9faa095427a62322b623ea450", + "subject_a.virusinterpreter.command.run:md5,1f81f6c9b31895d6b0e7ff0e68f2b942", "subject_a.virusinterpreter.command.sh:md5,5ad3b725b50b0f8237c6a4ba3a991570", "subject_a_subject_a.normal.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.bamtools.command.run:md5,2282059872d78fcb96be2081a17a0104", + "subject_a_subject_a.normal.bamtools.command.run:md5,c4d67804be48d922d61d38f21b05e0d7", "subject_a_subject_a.normal.bamtools.command.sh:md5,497cf77f9778b9cf5cb4204c06a8860c", "subject_a_subject_a.normal.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.redux.command.run:md5,171ef8b80e2ce3121f7177dfd62f0b00", + "subject_a_subject_a.normal.redux.command.run:md5,e7debb1765ad0aef03a6556f4fed42af", "subject_a_subject_a.normal.redux.command.sh:md5,73bcabd515e72b50c9e05624da40c60b", "subject_a_subject_a.tumor.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.bamtools.command.run:md5,48b2d08804c391cae4dcfdaec1705ab9", + "subject_a_subject_a.tumor.bamtools.command.run:md5,14e0adaca6d1a50fd9ff937cb53e2207", "subject_a_subject_a.tumor.bamtools.command.sh:md5,442b1e6b1e6a9dbe32326197ec8253bf", "subject_a_subject_a.tumor.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.cider.command.run:md5,5251254ccb8e2d4baf58d0a6b1cbaa5d", + "subject_a_subject_a.tumor.cider.command.run:md5,9c888699b1af22e9fed4c5baf961d451", "subject_a_subject_a.tumor.cider.command.sh:md5,80c5fda774fa9fb3ee613cd613f4ee00", "subject_a_subject_a.tumor.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.redux.command.run:md5,149f26486ed09e7ab6e688d74a0cc7c8", + "subject_a_subject_a.tumor.redux.command.run:md5,322fe8d84ed4fe89f23cfb643c44b0ca", "subject_a_subject_a.tumor.redux.command.sh:md5,f9324772e908bfdc70079a1aaf1680f4", "subject_a_subject_a.tumor_rna.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor_rna.cider.command.run:md5,7d678cefb25eb7236e0237694a0ce134", + "subject_a_subject_a.tumor_rna.cider.command.run:md5,2bfb1c987948050f8842769cd3719658", "subject_a_subject_a.tumor_rna.cider.command.sh:md5,d4e8146a5505ec387fcd591db4d2d56a", "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.pave.germline.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.pave.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.pave.somatic.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.pave.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.peach.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.peach.gene.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -745,182 +549,28 @@ "subject_a.tumor.purple.cnv.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.driver.catalog.germline.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.driver.catalog.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.purple.germline.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, "subject_a.tumor.purple.purity.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.qc:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.purple.somatic.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593808384, - "hidden": false, - "name": "subject_a.tumor.purple.sv.germline.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593808384 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593804288, - "hidden": false, - "name": "subject_a.tumor.purple.sv.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593804288 - }, "subject_a.normal.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.tumor.sage.germline.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, "subject_a.tumor.sage.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.tumor.sage.somatic.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, "subject_a.tumor.sage.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.normal.frag_lengths.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.normal.sage.append.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.tumor.frag_lengths.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.tumor.sage.append.vcf.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.teal.{tellength.tsv}:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "absolute": true, - "absolutePath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", - "canonicalPath": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", - "directory": false, - "file": true, - "freeSpace": 258593792000, - "hidden": false, - "name": "subject_a.tumor.teal.breakend.tsv.gz", - "parent": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal", - "path": "/Users/beatrizsavinhas/development/oncoflow/.nf-test/tests/4fda9f39bdb7e90a1a238b320a920a5a/output/oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", - "totalSpace": 994662584320, - "usableSpace": 258593792000 - }, "subject_a.tumor.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -929,7 +579,7 @@ "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-03T12:07:29.966578", + "timestamp": "2026-07-06T09:54:00.41671", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From df106115f89940135fd1ae2a254b00e99fb8f0a2 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 10:02:16 +0200 Subject: [PATCH 057/102] Update changelog. --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6af19ee..397d325 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Changed` -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to also ignore `pipeline_info` and `multiqc` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for run pipelines. ### `Fixed` From 09ccfb2e33210abde414d38f4c058ed25a5f1db7 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 10:02:51 +0200 Subject: [PATCH 058/102] Update changelog. --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 397d325..5145f85 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for run pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. ### `Fixed` From d4c0876c5ebbf73dd359ce29244d2e9ee3666ebd Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 10:15:31 +0200 Subject: [PATCH 059/102] Ignore .command.log in tests --- CHANGELOG.md | 1 + tests/.nftignore | 1 + tests/default.nf.test.snap | 36 +----------------------------------- 3 files changed, 3 insertions(+), 35 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5145f85..bfb87a2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.run` output files from `oncoanalyser` since they include the run directory which changes for each run and therefore cannot be snapshot. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. ### `Fixed` diff --git a/tests/.nftignore b/tests/.nftignore index 7dd0c11..c53f262 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -3,3 +3,4 @@ pipeline_info/*.{html,json,txt,yml} **/pipeline_info/*.{html,json,txt,yml} **/multiqc/** oncoanalyser/**/*.gz +oncoanalyser/**/*.command.run diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0ff16e4..ed211c0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -368,172 +368,138 @@ "subject_a.amber.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.amber.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.amber.command.run:md5,fc9d0a570871e2bb82ada7fe5109ed76", "subject_a.amber.command.sh:md5,ece04e00128d32c17f9348fe94e6f435", "subject_a.chord.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.chord.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.chord.command.run:md5,f7d8e437697e63f48733dc77331b30bd", "subject_a.chord.command.sh:md5,9b71409e679713e28b017824bc25c0bc", "subject_a.cobalt.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cobalt.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cobalt.command.run:md5,398ed5c2839a9ce225afe15f03795037", "subject_a.cobalt.command.sh:md5,249ff2daaf99134cd74d36683d00e52b", "subject_a.cuppa.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.cuppa.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cuppa.command.run:md5,e9e1b457f4fdfe0fe8691ae6b3552738", "subject_a.cuppa.command.sh:md5,7bc0af7c494aa796a0eb34875c76d4f7", "subject_a.esvee.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.esvee.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.esvee.command.run:md5,d8c3bf6adb24e390cb5ce819376465a0", "subject_a.esvee.command.sh:md5,3df68e38d29406d19e6dc0be882befd5", "subject_a.isofox.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.isofox.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.isofox.command.run:md5,78691a7d9b5874b2a96d97824f76c1fc", "subject_a.isofox.command.sh:md5,d8c9918ccfcfb4e26bcdded5466c7b14", "subject_a.lilac.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.lilac.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.lilac.command.run:md5,64c8db04b7af589b3e3a64735a0a91b4", "subject_a.lilac.command.sh:md5,067273b45d86fe02212dd41b074390b8", "subject_a.linx_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_germline.command.run:md5,91a0120ca2f85f79582430dd30f633ff", "subject_a.linx_germline.command.sh:md5,6810076ab4979a8a081283dea3ab65fa", "subject_a.linx_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_somatic.command.run:md5,d8de346206907980310c5ae3078e290b", "subject_a.linx_somatic.command.sh:md5,0be909d504771d4fb304bbc7680c2a00", "subject_a.linx_visualiser.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linx_visualiser.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_visualiser.command.run:md5,a1ad8de9ae1827b703c29b6ed5b3f137", "subject_a.linx_visualiser.command.sh:md5,b74ad1ea317fb89105326bd83666df3d", "subject_a.linxreport.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.linxreport.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linxreport.command.run:md5,bfb1f0210852ada894b4e2378495c25d", "subject_a.linxreport.command.sh:md5,82b46b4735acfc4a5f2777e0df80b183", "subject_a.neo_annotate_fusions.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_annotate_fusions.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_annotate_fusions.command.run:md5,6cceda3a4623f2448c8c6e09bc22a54b", "subject_a.neo_annotate_fusions.command.sh:md5,fc40ed44ab1936fea00a7a376ba6ed97", "subject_a.neo_finder.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_finder.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_finder.command.run:md5,b01e194ebdae2bb5b39af6500633dd77", "subject_a.neo_finder.command.sh:md5,d4d1109852cb5ffbc7d1dc5e312f3d98", "subject_a.neo_scorer.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.neo_scorer.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_scorer.command.run:md5,8bc4c25d0ef4634407fcf9dff4261e37", "subject_a.neo_scorer.command.sh:md5,072139d9fcee64b2638c13f0017c4fc7", "subject_a.orange.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.orange.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.orange.command.run:md5,33bd5c6c7dae6e4c176ab081dc0459bd", "subject_a.orange.command.sh:md5,939b1e1525c1aa3b5d7f75cc3b217f0e", "subject_a.pave_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_germline.command.run:md5,ed973db670b2313e67653637dbca2db1", "subject_a.pave_germline.command.sh:md5,343f61725ed8aca93842f860f40acffa", "subject_a.pave_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.pave_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_somatic.command.run:md5,ce1f736b2b41002035f8a6264b8cbbb6", "subject_a.pave_somatic.command.sh:md5,c3d4bc9ec34f6e33b3fe7f6fd7b00c3f", "subject_a.peach.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.peach.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.peach.command.run:md5,df2d1b71f1b523d5beb1762568568df8", "subject_a.peach.command.sh:md5,28b75a36763d0772d9d038c925aa569b", "subject_a.purple.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.purple.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.purple.command.run:md5,6b31d72e7e56c771b054d1d29c458965", "subject_a.purple.command.sh:md5,00f71a94eb7d3d3b4568db8abc522b5a", "subject_a.sage_append_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_germline.command.run:md5,52425702cc3ffc22fc20182b361ebb6e", "subject_a.sage_append_germline.command.sh:md5,b56a330cd442cae80fddf67e41b8e2e6", "subject_a.sage_append_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_append_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_somatic.command.run:md5,99f50da5a9774a9926f710b6e3fe4c37", "subject_a.sage_append_somatic.command.sh:md5,fbc57d331e476b200e34afd53ef1e40a", "subject_a.sage_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_germline.command.run:md5,7e8f4fb054ce4a014382a055792a95e0", "subject_a.sage_germline.command.sh:md5,8a36236f7235dd2f852d280fc8e96b78", "subject_a.sage_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sage_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_somatic.command.run:md5,c49f6502e2f6893878eeb16a41227b23", "subject_a.sage_somatic.command.sh:md5,b49e27b48f909890e9b94016e1f38caf", "subject_a.sigs.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.sigs.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sigs.command.run:md5,cf307f3570167466b7f5d20da28d7e93", "subject_a.sigs.command.sh:md5,6008af259edb80b5fd5b966e35f69dc5", "subject_a.teal_pipeline.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_pipeline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_pipeline.command.run:md5,cb35186b76e6ece19c8f2516afc1e58e", "subject_a.teal_pipeline.command.sh:md5,6d050b9ecdc8f3e5568c54548a609e97", "subject_a.teal_prep.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.teal_prep.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_prep.command.run:md5,6e45bb5ddd579542fc47e7c6f04891e0", "subject_a.teal_prep.command.sh:md5,cc5e17ec71fe1a5d768c71862ad95ec5", "subject_a.virusbreakend.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusbreakend.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusbreakend.command.run:md5,5e2505af840239aeefd0dbc77f3ad74f", "subject_a.virusbreakend.command.sh:md5,38c53328ed48069a23b3855f325901c7", "subject_a.virusinterpreter.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a.virusinterpreter.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusinterpreter.command.run:md5,1f81f6c9b31895d6b0e7ff0e68f2b942", "subject_a.virusinterpreter.command.sh:md5,5ad3b725b50b0f8237c6a4ba3a991570", "subject_a_subject_a.normal.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.bamtools.command.run:md5,c4d67804be48d922d61d38f21b05e0d7", "subject_a_subject_a.normal.bamtools.command.sh:md5,497cf77f9778b9cf5cb4204c06a8860c", "subject_a_subject_a.normal.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.normal.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.redux.command.run:md5,e7debb1765ad0aef03a6556f4fed42af", "subject_a_subject_a.normal.redux.command.sh:md5,73bcabd515e72b50c9e05624da40c60b", "subject_a_subject_a.tumor.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.bamtools.command.run:md5,14e0adaca6d1a50fd9ff937cb53e2207", "subject_a_subject_a.tumor.bamtools.command.sh:md5,442b1e6b1e6a9dbe32326197ec8253bf", "subject_a_subject_a.tumor.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.cider.command.run:md5,9c888699b1af22e9fed4c5baf961d451", "subject_a_subject_a.tumor.cider.command.sh:md5,80c5fda774fa9fb3ee613cd613f4ee00", "subject_a_subject_a.tumor.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.redux.command.run:md5,322fe8d84ed4fe89f23cfb643c44b0ca", "subject_a_subject_a.tumor.redux.command.sh:md5,f9324772e908bfdc70079a1aaf1680f4", "subject_a_subject_a.tumor_rna.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", "subject_a_subject_a.tumor_rna.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor_rna.cider.command.run:md5,2bfb1c987948050f8842769cd3719658", "subject_a_subject_a.tumor_rna.cider.command.sh:md5,d4e8146a5505ec387fcd591db4d2d56a", "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -579,7 +545,7 @@ "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-06T09:54:00.41671", + "timestamp": "2026-07-06T10:06:51.25115", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 898808d9b23c7edc0d25af43c219a34965f01546 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 10:35:18 +0200 Subject: [PATCH 060/102] Ignore all .command.* files in tests --- CHANGELOG.md | 2 +- tests/.nftignore | 2 +- tests/default.nf.test.snap | 138 +------------------------------------ 3 files changed, 3 insertions(+), 139 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bfb87a2..0f48c0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.run` output files from `oncoanalyser` since they include the run directory which changes for each run and therefore cannot be snapshot. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. ### `Fixed` diff --git a/tests/.nftignore b/tests/.nftignore index c53f262..622332c 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -3,4 +3,4 @@ pipeline_info/*.{html,json,txt,yml} **/pipeline_info/*.{html,json,txt,yml} **/multiqc/** oncoanalyser/**/*.gz -oncoanalyser/**/*.command.run +oncoanalyser/**/*.command.* diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ed211c0..b8077b8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -365,142 +365,6 @@ "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor_linx.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.amber.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.amber.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.amber.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.amber.command.sh:md5,ece04e00128d32c17f9348fe94e6f435", - "subject_a.chord.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.chord.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.chord.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.chord.command.sh:md5,9b71409e679713e28b017824bc25c0bc", - "subject_a.cobalt.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.cobalt.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.cobalt.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cobalt.command.sh:md5,249ff2daaf99134cd74d36683d00e52b", - "subject_a.cuppa.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.cuppa.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.cuppa.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.cuppa.command.sh:md5,7bc0af7c494aa796a0eb34875c76d4f7", - "subject_a.esvee.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.esvee.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.esvee.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.esvee.command.sh:md5,3df68e38d29406d19e6dc0be882befd5", - "subject_a.isofox.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.isofox.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.isofox.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.isofox.command.sh:md5,d8c9918ccfcfb4e26bcdded5466c7b14", - "subject_a.lilac.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.lilac.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.lilac.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.lilac.command.sh:md5,067273b45d86fe02212dd41b074390b8", - "subject_a.linx_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_germline.command.sh:md5,6810076ab4979a8a081283dea3ab65fa", - "subject_a.linx_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_somatic.command.sh:md5,0be909d504771d4fb304bbc7680c2a00", - "subject_a.linx_visualiser.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_visualiser.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linx_visualiser.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linx_visualiser.command.sh:md5,b74ad1ea317fb89105326bd83666df3d", - "subject_a.linxreport.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linxreport.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.linxreport.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.linxreport.command.sh:md5,82b46b4735acfc4a5f2777e0df80b183", - "subject_a.neo_annotate_fusions.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_annotate_fusions.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_annotate_fusions.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_annotate_fusions.command.sh:md5,fc40ed44ab1936fea00a7a376ba6ed97", - "subject_a.neo_finder.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_finder.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_finder.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_finder.command.sh:md5,d4d1109852cb5ffbc7d1dc5e312f3d98", - "subject_a.neo_scorer.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_scorer.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.neo_scorer.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.neo_scorer.command.sh:md5,072139d9fcee64b2638c13f0017c4fc7", - "subject_a.orange.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.orange.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.orange.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.orange.command.sh:md5,939b1e1525c1aa3b5d7f75cc3b217f0e", - "subject_a.pave_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.pave_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.pave_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_germline.command.sh:md5,343f61725ed8aca93842f860f40acffa", - "subject_a.pave_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.pave_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.pave_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.pave_somatic.command.sh:md5,c3d4bc9ec34f6e33b3fe7f6fd7b00c3f", - "subject_a.peach.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.peach.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.peach.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.peach.command.sh:md5,28b75a36763d0772d9d038c925aa569b", - "subject_a.purple.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.purple.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.purple.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.purple.command.sh:md5,00f71a94eb7d3d3b4568db8abc522b5a", - "subject_a.sage_append_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_append_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_append_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_germline.command.sh:md5,b56a330cd442cae80fddf67e41b8e2e6", - "subject_a.sage_append_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_append_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_append_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_append_somatic.command.sh:md5,fbc57d331e476b200e34afd53ef1e40a", - "subject_a.sage_germline.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_germline.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_germline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_germline.command.sh:md5,8a36236f7235dd2f852d280fc8e96b78", - "subject_a.sage_somatic.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_somatic.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sage_somatic.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sage_somatic.command.sh:md5,b49e27b48f909890e9b94016e1f38caf", - "subject_a.sigs.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sigs.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.sigs.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.sigs.command.sh:md5,6008af259edb80b5fd5b966e35f69dc5", - "subject_a.teal_pipeline.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.teal_pipeline.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.teal_pipeline.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_pipeline.command.sh:md5,6d050b9ecdc8f3e5568c54548a609e97", - "subject_a.teal_prep.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.teal_prep.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.teal_prep.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.teal_prep.command.sh:md5,cc5e17ec71fe1a5d768c71862ad95ec5", - "subject_a.virusbreakend.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.virusbreakend.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.virusbreakend.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusbreakend.command.sh:md5,38c53328ed48069a23b3855f325901c7", - "subject_a.virusinterpreter.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.virusinterpreter.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a.virusinterpreter.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.virusinterpreter.command.sh:md5,5ad3b725b50b0f8237c6a4ba3a991570", - "subject_a_subject_a.normal.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.normal.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.normal.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.bamtools.command.sh:md5,497cf77f9778b9cf5cb4204c06a8860c", - "subject_a_subject_a.normal.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.normal.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.normal.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.normal.redux.command.sh:md5,73bcabd515e72b50c9e05624da40c60b", - "subject_a_subject_a.tumor.bamtools.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.bamtools.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.bamtools.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.bamtools.command.sh:md5,442b1e6b1e6a9dbe32326197ec8253bf", - "subject_a_subject_a.tumor.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.cider.command.sh:md5,80c5fda774fa9fb3ee613cd613f4ee00", - "subject_a_subject_a.tumor.redux.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.redux.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor.redux.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor.redux.command.sh:md5,f9324772e908bfdc70079a1aaf1680f4", - "subject_a_subject_a.tumor_rna.cider.command.err:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor_rna.cider.command.log:md5,ddf651020afae06c28be5d3e3365874c", - "subject_a_subject_a.tumor_rna.cider.command.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a_subject_a.tumor_rna.cider.command.sh:md5,d4e8146a5505ec387fcd591db4d2d56a", "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.orange.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -545,7 +409,7 @@ "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-06T10:06:51.25115", + "timestamp": "2026-07-06T10:35:01.939539", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From edb0d1f5b16140655bf3d7755a1b019d682494f3 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 11:11:45 +0200 Subject: [PATCH 061/102] Create oncoanalyser named parameters. --- conf/test.config | 2 +- main.nf | 12 ++++++++++++ nextflow.config | 8 ++++---- workflows/oncoflow.nf | 12 ++++++++---- 4 files changed, 25 insertions(+), 9 deletions(-) diff --git a/conf/test.config b/conf/test.config index e31fb65..b721785 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,5 +22,5 @@ params { config_profile_name = 'Test profile (stub runs for all pipelines)' config_profile_description = 'Minimal test where all pipelines are run in stub mode to check that pipelines are run sequentially' - oncoanalyser.nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' + oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } diff --git a/main.nf b/main.nf index 32a7c11..8ff708e 100644 --- a/main.nf +++ b/main.nf @@ -27,6 +27,10 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: + oncoanalyser_additional_config + oncoanalyser_nextflow_opts + oncoanalyser_params_file + oncoanalyser_samplesheet outdir // string: The output directory where the results will be saved main: @@ -35,6 +39,10 @@ workflow CLINICALGENOMICS_ONCOFLOW { // WORKFLOW: Run pipeline // ONCOFLOW ( + oncoanalyser_additional_config, + oncoanalyser_nextflow_opts, + oncoanalyser_params_file, + oncoanalyser_samplesheet, outdir, ) @@ -68,6 +76,10 @@ workflow { // WORKFLOW: Run main workflow // CLINICALGENOMICS_ONCOFLOW ( + params.oncoanalyser_additional_config, + params.oncoanalyser_nextflow_opts, + params.oncoanalyser_params_file, + params.oncoanalyser_samplesheet, params.outdir ) diff --git a/nextflow.config b/nextflow.config index 6dab9ce..ed90a66 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,10 +10,10 @@ params { // Oncoanalyser input parameters - oncoanalyser.nextflow_opts = '' - oncoanalyser.params_file = '' - oncoanalyser.samplesheet = '' - oncoanalyser.additional_config = '' + oncoanalyser_nextflow_opts = '' + oncoanalyser_params_file = '' + oncoanalyser_samplesheet = '' + oncoanalyser_additional_config = '' // Boilerplate options outdir = null diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index acb2d16..aee7689 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -15,6 +15,10 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: + oncoanalyser_additional_config + oncoanalyser_nextflow_opts + oncoanalyser_params_file + oncoanalyser_samplesheet outdir main: @@ -23,10 +27,10 @@ workflow ONCOFLOW { NFCORE_ONCOANALYSER( 'nf-core/oncoanalyser', - params.oncoanalyser.nextflow_opts, - params.oncoanalyser.params_file, - params.oncoanalyser.samplesheet, - params.oncoanalyser.additional_config, + oncoanalyser_nextflow_opts, + oncoanalyser_params_file, + oncoanalyser_samplesheet, + oncoanalyser_additional_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) From 8269760956e12490d32da18f0883df1420ac1d26 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 11:14:56 +0200 Subject: [PATCH 062/102] Refiner nextflow_schema, organise input parameters and add info strings in take blocks. --- docs/parameters.md | 11 +++++++++++ main.nf | 12 ++++++------ nextflow.config | 2 +- nextflow_schema.json | 41 +++++++++++++++++++++++++++++++++++++++++ workflows/oncoflow.nf | 26 +++++++++++++------------- 5 files changed, 72 insertions(+), 20 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index 3892a92..dde6322 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -2,6 +2,17 @@ Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow. +## Oncoanalyser + +Necessary input files and nextflow options for running nf-core/oncoanlyser. + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `oncoanalyser_additional_config` | Path to additional config file for nf-core/oncoanlyser (optional). | `string` | | | | +| `oncoanalyser_nextflow_opts` | Nextflow options for running nf-core/oncoanlyser. | `string` | | True | | +| `oncoanalyser_params_file` | Path to params file for nf-core/oncoanlyser. | `string` | | | | +| `oncoanalyser_samplesheet` | Path to csv samplesheet file for nf-core/oncoanalyser. | `string` | | | | + ## Input/output options Define where the pipeline should find input data and save output data. diff --git a/main.nf b/main.nf index 8ff708e..291663d 100644 --- a/main.nf +++ b/main.nf @@ -27,11 +27,11 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: - oncoanalyser_additional_config - oncoanalyser_nextflow_opts - oncoanalyser_params_file - oncoanalyser_samplesheet - outdir // string: The output directory where the results will be saved + oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline + oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -43,7 +43,7 @@ workflow CLINICALGENOMICS_ONCOFLOW { oncoanalyser_nextflow_opts, oncoanalyser_params_file, oncoanalyser_samplesheet, - outdir, + outdir ) emit: diff --git a/nextflow.config b/nextflow.config index ed90a66..2b37708 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,10 +10,10 @@ params { // Oncoanalyser input parameters + oncoanalyser_additional_config = '' oncoanalyser_nextflow_opts = '' oncoanalyser_params_file = '' oncoanalyser_samplesheet = '' - oncoanalyser_additional_config = '' // Boilerplate options outdir = null diff --git a/nextflow_schema.json b/nextflow_schema.json index dfbfead..d38ffe8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -5,6 +5,44 @@ "description": "Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow.", "type": "object", "$defs": { + "oncoanalyser": { + "title": "Oncoanalyser", + "type": "object", + "description": "Necessary input files and nextflow options for running nf-core/oncoanlyser.", + "default": "", + "properties": { + "oncoanalyser_additional_config": { + "type": "string", + "description": "Path to additional config file for nf-core/oncoanlyser (optional).", + "format": "file-path", + "exists": true, + "fa_icon": "far fa-file" + }, + "oncoanalyser_nextflow_opts": { + "type": "string", + "description": "Nextflow options for running nf-core/oncoanlyser.", + "fa_icon": "fas fa-terminal" + }, + "oncoanalyser_params_file": { + "type": "string", + "description": "Path to params file for nf-core/oncoanlyser.", + "format": "file-path", + "exists": true, + "fa_icon": "fas fa-file" + }, + "oncoanalyser_samplesheet": { + "type": "string", + "description": "Path to csv samplesheet file for nf-core/oncoanalyser.", + "format": "file-path", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "exists": true, + "fa_icon": "fas fa-file-csv" + } + }, + "required": ["oncoanalyser_nextflow_opts"], + "fa_icon": "fas fa-file-import" + }, "input_output_options": { "title": "Input/output options", "type": "object", @@ -153,6 +191,9 @@ } }, "allOf": [ + { + "$ref": "#/$defs/oncoanalyser" + }, { "$ref": "#/$defs/input_output_options" }, diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index aee7689..84e71be 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -15,11 +15,11 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: - oncoanalyser_additional_config - oncoanalyser_nextflow_opts - oncoanalyser_params_file - oncoanalyser_samplesheet - outdir + oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline + oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -54,14 +54,14 @@ workflow ONCOFLOW { "${process}:\n${tool_versions.join('\n')}" } - def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) - .mix(topic_versions_string) - .collectFile( - storeDir: "${outdir}/pipeline_info", - name: 'oncoflow_software_' + 'versions.yml', - sort: true, - newLine: true - ) + // def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + // .mix(topic_versions_string) + // .collectFile( + // storeDir: "${outdir}/pipeline_info", + // name: 'oncoflow_software_' + 'versions.yml', + // sort: true, + // newLine: true + // ) emit: oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [ path(analysis_output_directory) ] From 6f21598777fb62681232b9ff8d7e03a3a6315710 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 11:20:31 +0200 Subject: [PATCH 063/102] Update changelog. --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0f48c0f..ce3b98b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,9 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` -- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. +- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) Added `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_additional_config`, `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. ### `Changed` From 2479a3f939a7e725ca70b984511e308270f7df15 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 11:24:50 +0200 Subject: [PATCH 064/102] Remove commented out code. --- workflows/oncoflow.nf | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 84e71be..f6c7b8f 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -54,14 +54,14 @@ workflow ONCOFLOW { "${process}:\n${tool_versions.join('\n')}" } - // def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) - // .mix(topic_versions_string) - // .collectFile( - // storeDir: "${outdir}/pipeline_info", - // name: 'oncoflow_software_' + 'versions.yml', - // sort: true, - // newLine: true - // ) + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + .mix(topic_versions_string) + .collectFile( + storeDir: "${outdir}/pipeline_info", + name: 'oncoflow_software_' + 'versions.yml', + sort: true, + newLine: true + ) emit: oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [ path(analysis_output_directory) ] From 5c5c704f9ff3a501d25ab3bfe11f88a6b540345f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 13:37:44 +0200 Subject: [PATCH 065/102] Style: refactor info strings. --- main.nf | 2 +- workflows/oncoflow.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 291663d..e55fe7f 100644 --- a/main.nf +++ b/main.nf @@ -47,7 +47,7 @@ workflow CLINICALGENOMICS_ONCOFLOW { ) emit: - oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [ path(analysis_output_directory) ] + oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(oncoanalyser_output_directory)] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index f6c7b8f..2448293 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -64,7 +64,7 @@ workflow ONCOFLOW { ) emit: - oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [ path(analysis_output_directory) ] + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] versions = ch_versions // channel: [ path(versions.yml) ] } From 39414898575e9acfb168b806a4e2aa86f5247239 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 15:17:32 +0200 Subject: [PATCH 066/102] Add CREATE_ONCOREFINER_PARAMS_FILE local module. --- .../local/createoncorefinerparamsfile/main.nf | 61 +++++++++++++++++ .../createoncorefinerparamsfile/meta.yml | 68 +++++++++++++++++++ .../tests/main.nf.test | 65 ++++++++++++++++++ .../tests/main.nf.test.snap | 65 ++++++++++++++++++ 4 files changed, 259 insertions(+) create mode 100644 modules/local/createoncorefinerparamsfile/main.nf create mode 100644 modules/local/createoncorefinerparamsfile/meta.yml create mode 100644 modules/local/createoncorefinerparamsfile/tests/main.nf.test create mode 100644 modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf new file mode 100644 index 0000000..50a684b --- /dev/null +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -0,0 +1,61 @@ +process CREATE_ONCOREFINER_PARAMS_FILE { + tag 'oncorefiner' + label 'process_single' + + input: + val case_id + val subject_id + val sample_id_tumor + val sample_id_normal + val sex + path oncoanalyser_results_dir + + output: + + path "oncorefiner_params.yaml", emit: params_file + // WARN: Please update version string when the module is updated. + tuple val("${task.process}"), val('createoncorefinerparamsfile'), val('1.0'), topic: versions, emit: versions_createoncorefinerparamsfile + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + + def path_snv_vcf = oncoanalyser_results_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") + def path_sv_vcf = oncoanalyser_results_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") + def path_bam_tumor = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") + def path_bai_tumor = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") + def path_bam_normal = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") + def path_bai_normal = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") + + + def oncorefiner_params_file = + [ + "\"case_id: ${case_id}", + "sample_id_tumor: ${sample_id_tumor}", + "sample_id_normal: ${sample_id_normal}", + "sex: ${sex}", + "snv_vcf: ${path_snv_vcf}", + "sv_vcf: ${path_sv_vcf}", + "bam_tumor: ${path_bam_tumor}", + "bai_tumor: ${path_bai_tumor}", + "bam_normal: ${path_bam_normal}", + "bai_normal: ${path_bai_normal}\"" + ].join("\\n") + + """ + echo $args + + printf $oncorefiner_params_file > oncorefiner_params.yaml + """ + + stub: + def args = task.ext.args ?: '' + + """ + echo $args + + touch oncorefiner_params.yaml + """ +} diff --git a/modules/local/createoncorefinerparamsfile/meta.yml b/modules/local/createoncorefinerparamsfile/meta.yml new file mode 100644 index 0000000..d2b97e6 --- /dev/null +++ b/modules/local/createoncorefinerparamsfile/meta.yml @@ -0,0 +1,68 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +# # TODO nf-core: Add a description of the module and list keywords +name: "createoncorefinerparamsfile" +description: write your description here +keywords: + - samplesheet + - oncoanalyser + - oncorefiner +tools: + - "createoncorefinerparamsfile": + description: "Generate a parameters file for the oncorefiner pipeline based on the output of the oncoanalyser pipeline." + homepage: "" + documentation: "" + tool_dev_url: "" + doi: "" + licence: null + identifier: null + +input: + - case_id: + type: string + description: Case ID + - subject_id: + type: string + description: Subject ID + - sample_id_tumor: + type: string + description: Sample ID of the tumor sample + - sample_id_normal: + type: string + description: Sample ID of the normal sample + - sex: + type: string + description: Sex of the patient + - oncoanalyser_results_dir: + type: directory + description: Path to the output directory of the oncoanalyser pipeline +output: + parameters_file: + - "oncorefiner_params.yaml": + type: file + description: Parameters file for the oncorefiner pipeline + pattern: "oncorefiner_params.yaml" + versions_createoncorefinerparamsfile: + - - ${task.process}: + type: string + description: The name of the process + - createoncorefinerparamsfile: + type: string + description: The name of the tool + - "1.0": + type: string + description: The version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - createoncorefinerparamsfile: + type: string + description: The name of the tool + - "1.0": + type: string + description: The version of the tool +authors: + - "@beatrizsavinhas" +maintainers: + - "@beatrizsavinhas" diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test new file mode 100644 index 0000000..ca33016 --- /dev/null +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -0,0 +1,65 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core modules test createoncorefinerparamsfile +nextflow_process { + + name "Test Process CREATE_ONCOREFINER_PARAMS_FILE" + script "../main.nf" + process "CREATE_ONCOREFINER_PARAMS_FILE" + + tag "modules" + tag "create_oncorefiner_params_file" + + test("Given a valid oncoanalyser results directory") { + + when { + process { + """ + input[0] = "test_case_id" + input[1] = "test_subject_id" + input[2] = "test_sample_id_tumor" + input[3] = "test_sample_id_normal" + input[4] = "female" + input[5] = "$projectDir" + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + file(process.out.params_file[0]).text + ).match() } + ) + } + + } + + test("-stub") { + + options "-stub" + + when { + process { + """ + input[0] = "test_case_id" + input[1] = "test_subject_id" + input[2] = "test_sample_id_tumor" + input[3] = "test_sample_id_normal" + input[4] = "female" + input[5] = "$projectDir" + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap new file mode 100644 index 0000000..e90a7e0 --- /dev/null +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "Given a valid oncoanalyser results directory": { + "content": [ + { + "0": [ + "oncorefiner_params.yaml:md5,9c981227175e6d0573daa67c7a91a311" + ], + "1": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ], + "params_file": [ + "oncorefiner_params.yaml:md5,9c981227175e6d0573daa67c7a91a311" + ], + "versions_createoncorefinerparamsfile": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ] + }, + "case_id: test_case_id\nsample_id_tumor: test_sample_id_tumor\nsample_id_normal: test_sample_id_normal\nsex: female\nsnv_vcf: oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz\nsv_vcf: oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz\nbam_tumor: oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam\nbai_tumor: oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai\nbam_normal: oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam\nbai_normal: oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + ], + "timestamp": "2026-07-06T15:00:57.203386", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "-stub": { + "content": [ + { + "0": [ + "oncorefiner_params.yaml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ], + "params_file": [ + "oncorefiner_params.yaml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions_createoncorefinerparamsfile": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ] + } + ], + "timestamp": "2026-07-06T14:09:16.928105", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From a6ef6032964ff6de5e7f7d3e2492364bc8754d22 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 15:26:18 +0200 Subject: [PATCH 067/102] Change notation for take blocks to use . --- main.nf | 18 +++++++++--------- workflows/oncoflow.nf | 18 +++++++++--------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/main.nf b/main.nf index e55fe7f..39677a8 100644 --- a/main.nf +++ b/main.nf @@ -27,11 +27,11 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: - oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline - oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline - oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline - oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - outdir // string: [mandatory] The output directory where the results will be saved + val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -39,10 +39,10 @@ workflow CLINICALGENOMICS_ONCOFLOW { // WORKFLOW: Run pipeline // ONCOFLOW ( - oncoanalyser_additional_config, - oncoanalyser_nextflow_opts, - oncoanalyser_params_file, - oncoanalyser_samplesheet, + val_oncoanalyser_additional_config, + val_oncoanalyser_nextflow_opts, + val_oncoanalyser_params_file, + val_oncoanalyser_samplesheet, outdir ) diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 2448293..1f56b2b 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -15,11 +15,11 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: - oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline - oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline - oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline - oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - outdir // string: [mandatory] The output directory where the results will be saved + val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -27,10 +27,10 @@ workflow ONCOFLOW { NFCORE_ONCOANALYSER( 'nf-core/oncoanalyser', - oncoanalyser_nextflow_opts, - oncoanalyser_params_file, - oncoanalyser_samplesheet, - oncoanalyser_additional_config, + val_oncoanalyser_nextflow_opts, + val_oncoanalyser_params_file, + val_oncoanalyser_samplesheet, + val_oncoanalyser_additional_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) From 4392a60360d77ed5febdf713275a2132c2898972 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 15:38:40 +0200 Subject: [PATCH 068/102] Add metadata parameters. --- conf/test.config | 8 ++++++++ docs/parameters.md | 12 ++++++++++++ nextflow.config | 7 +++++++ nextflow_schema.json | 34 ++++++++++++++++++++++++++++++++++ 4 files changed, 61 insertions(+) diff --git a/conf/test.config b/conf/test.config index b721785..9123fff 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,5 +22,13 @@ params { config_profile_name = 'Test profile (stub runs for all pipelines)' config_profile_description = 'Minimal test where all pipelines are run in stub mode to check that pipelines are run sequentially' + // Metadata + case_id = 'test_case_id' + sample_id_tumor = 'test_sample_id_tumor' + sample_id_normal = 'test_sample_id_normal' + subject_id = 'test_subject_id' + sex = 'female' + + // Oncoanalyser input parameters oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } diff --git a/docs/parameters.md b/docs/parameters.md index dde6322..1004b4d 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -2,6 +2,18 @@ Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow. +## Metadata + + + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `case_id` | Case ID. | `string` | | True | | +| `sample_id_tumor` | Sample id of the tumor sample. | `string` | | True | | +| `sample_id_normal` | Sample id of the normal sample. | `string` | | True | | +| `subject_id` | Subject ID of the patient. | `string` | | True | | +| `sex` | Sex of the patient. (accepted: `female`\|`male`\|`unknown`) | `string` | | True | | + ## Oncoanalyser Necessary input files and nextflow options for running nf-core/oncoanlyser. diff --git a/nextflow.config b/nextflow.config index 2b37708..e9e62cb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,6 +9,13 @@ // Global default params, used in configs params { + // Metadata + case_id = '' + sample_id_tumor = '' + sample_id_normal = '' + subject_id = '' + sex = '' + // Oncoanalyser input parameters oncoanalyser_additional_config = '' oncoanalyser_nextflow_opts = '' diff --git a/nextflow_schema.json b/nextflow_schema.json index d38ffe8..3b21636 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -5,6 +5,37 @@ "description": "Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow.", "type": "object", "$defs": { + "metadata": { + "title": "Metadata", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-info-circle", + "properties": { + "case_id": { + "type": "string", + "description": "Case ID." + }, + "sample_id_tumor": { + "type": "string", + "description": "Sample id of the tumor sample." + }, + "sample_id_normal": { + "type": "string", + "description": "Sample id of the normal sample." + }, + "subject_id": { + "type": "string", + "description": "Subject ID of the patient." + }, + "sex": { + "type": "string", + "enum": ["female", "male", "unknown"], + "description": "Sex of the patient." + } + }, + "required": ["sex", "subject_id", "sample_id_normal", "sample_id_tumor", "case_id"] + }, "oncoanalyser": { "title": "Oncoanalyser", "type": "object", @@ -191,6 +222,9 @@ } }, "allOf": [ + { + "$ref": "#/$defs/metadata" + }, { "$ref": "#/$defs/oncoanalyser" }, From a553d4448fe5dcce40d5489622d7a4a8acb8b788 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 15:48:40 +0200 Subject: [PATCH 069/102] Publish oncorefiner params file. --- main.nf | 25 +++++++++++++++++++++++-- tests/default.nf.test.snap | 7 +++++-- workflows/oncoflow.nf | 21 ++++++++++++++++++--- 3 files changed, 46 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index 39677a8..2b28c19 100644 --- a/main.nf +++ b/main.nf @@ -27,10 +27,15 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: + val_case_id // string: [mandatory] Case ID val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample + val_sample_id_normal // string: [mandatory] Sample ID of the normal sample + val_subject_id // string: [mandatory] Subject ID + val_sex // string: [mandatory] Sex of the patient outdir // string: [mandatory] The output directory where the results will be saved main: @@ -39,15 +44,22 @@ workflow CLINICALGENOMICS_ONCOFLOW { // WORKFLOW: Run pipeline // ONCOFLOW ( + val_case_id, val_oncoanalyser_additional_config, val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, + val_sample_id_tumor, + val_sample_id_normal, + val_subject_id, + val_sex, outdir ) emit: - oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(oncoanalyser_output_directory)] + oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(oncoanalyser_output_directory)] + oncorefiner_params_file = ONCOFLOW.out.oncorefiner_params_file // channel: [path(yaml)] + } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -76,10 +88,15 @@ workflow { // WORKFLOW: Run main workflow // CLINICALGENOMICS_ONCOFLOW ( + params.case_id, params.oncoanalyser_additional_config, params.oncoanalyser_nextflow_opts, params.oncoanalyser_params_file, params.oncoanalyser_samplesheet, + params.sample_id_tumor, + params.sample_id_normal, + params.subject_id, + params.sex, params.outdir ) @@ -95,13 +112,17 @@ workflow { ) publish: - oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.out.oncoanalyser_output + oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.out.oncoanalyser_output + oncorefiner_params_file = CLINICALGENOMICS_ONCOFLOW.out.oncorefiner_params_file } output { oncoanalyser_output { path "oncoanalyser" } + oncorefiner_params_file { + path "oncorefiner" + } } /* diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b8077b8..00830d6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -322,6 +322,8 @@ "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.virusbreakend.vcf", "oncoanalyser/results/subject_a/virusinterpreter", "oncoanalyser/results/subject_a/virusinterpreter/subject_a.tumor.virus.annotated.tsv", + "oncorefiner", + "oncorefiner/oncorefiner_params.yaml", "pipeline_info", "pipeline_info/oncoflow_software_versions.yml" ], @@ -406,10 +408,11 @@ "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "oncorefiner_params.yaml:md5,28d103d129e8e5d8ea672a7f7186d9d8" ] ], - "timestamp": "2026-07-06T10:35:01.939539", + "timestamp": "2026-07-06T15:47:38.825724", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 1f56b2b..78a90b0 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -4,7 +4,8 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { CREATE_ONCOREFINER_PARAMS_FILE } from "../modules/local/createoncorefinerparamsfile/main" +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15,10 +16,15 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: + val_case_id // string: [mandatory] Case ID val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample + val_sample_id_normal // string: [mandatory] Sample ID of the normal sample + val_subject_id // string: [mandatory] Subject ID + val_sex // string: [mandatory] Sex of the patient outdir // string: [mandatory] The output directory where the results will be saved main: @@ -34,6 +40,14 @@ workflow ONCOFLOW { workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) + CREATE_ONCOREFINER_PARAMS_FILE( + val_case_id, + val_subject_id, + val_sample_id_tumor, + val_sample_id_normal, + val_sex, + NFCORE_ONCOANALYSER.out.output) + // // Collate and save software versions // @@ -64,8 +78,9 @@ workflow ONCOFLOW { ) emit: - oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] - versions = ch_versions // channel: [ path(versions.yml) ] + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] + oncorefiner_params_file = CREATE_ONCOREFINER_PARAMS_FILE.out.params_file // channel: [path(yaml)] + versions = ch_versions } /* From f712510decd997698343ebc4d6bc585438a2073b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 16:42:23 +0200 Subject: [PATCH 070/102] Fix bug with relative paths in params file. --- modules/local/createoncorefinerparamsfile/main.nf | 14 ++++++++------ workflows/oncoflow.nf | 4 +++- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf index 50a684b..c47b645 100644 --- a/modules/local/createoncorefinerparamsfile/main.nf +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -9,6 +9,7 @@ process CREATE_ONCOREFINER_PARAMS_FILE { val sample_id_normal val sex path oncoanalyser_results_dir + val outdir output: @@ -22,13 +23,14 @@ process CREATE_ONCOREFINER_PARAMS_FILE { script: def args = task.ext.args ?: '' - def path_snv_vcf = oncoanalyser_results_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") - def path_sv_vcf = oncoanalyser_results_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") - def path_bam_tumor = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") - def path_bai_tumor = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") - def path_bam_normal = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") - def path_bai_normal = oncoanalyser_results_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") + def oncoanalyser_output_dir = file(outdir).resolve("oncoanalyser/${oncoanalyser_results_dir}") + def path_snv_vcf = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") + def path_sv_vcf = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") + def path_bam_tumor = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") + def path_bai_tumor = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") + def path_bam_normal = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") + def path_bai_normal = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") def oncorefiner_params_file = [ diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 78a90b0..eed4f77 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -46,7 +46,9 @@ workflow ONCOFLOW { val_sample_id_tumor, val_sample_id_normal, val_sex, - NFCORE_ONCOANALYSER.out.output) + NFCORE_ONCOANALYSER.out.output, + outdir + ) // // Collate and save software versions From f2742ca7549b51a8c974aaa719b911d4f4928084 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 16:42:46 +0200 Subject: [PATCH 071/102] Update subject_id to match test data from oncoanalyser. --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 9123fff..d3d3b3b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,7 +26,7 @@ params { case_id = 'test_case_id' sample_id_tumor = 'test_sample_id_tumor' sample_id_normal = 'test_sample_id_normal' - subject_id = 'test_subject_id' + subject_id = 'subject_a' // matches the subject_id in the sample sheet of the test data of the oncoanalyser pipeline sex = 'female' // Oncoanalyser input parameters From 6344ed8a4b015de51fee316b3fa4d7aa0a5c7c63 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 16:50:53 +0200 Subject: [PATCH 072/102] Update module test and snapshot. --- .../local/createoncorefinerparamsfile/tests/main.nf.test | 5 +++-- .../createoncorefinerparamsfile/tests/main.nf.test.snap | 9 ++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index ca33016..1332e91 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -20,6 +20,7 @@ nextflow_process { input[3] = "test_sample_id_normal" input[4] = "female" input[5] = "$projectDir" + input[6] = "test_outdir" """ } } @@ -28,8 +29,7 @@ nextflow_process { assert process.success assertAll( { assert snapshot( - process.out, - file(process.out.params_file[0]).text + process.out ).match() } ) } @@ -49,6 +49,7 @@ nextflow_process { input[3] = "test_sample_id_normal" input[4] = "female" input[5] = "$projectDir" + input[6] = "test_outdir" """ } } diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap index e90a7e0..e3b14aa 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -3,7 +3,7 @@ "content": [ { "0": [ - "oncorefiner_params.yaml:md5,9c981227175e6d0573daa67c7a91a311" + "oncorefiner_params.yaml:md5,2f1b615720d5629714cf3e237faffa60" ], "1": [ [ @@ -13,7 +13,7 @@ ] ], "params_file": [ - "oncorefiner_params.yaml:md5,9c981227175e6d0573daa67c7a91a311" + "oncorefiner_params.yaml:md5,2f1b615720d5629714cf3e237faffa60" ], "versions_createoncorefinerparamsfile": [ [ @@ -22,10 +22,9 @@ "1.0" ] ] - }, - "case_id: test_case_id\nsample_id_tumor: test_sample_id_tumor\nsample_id_normal: test_sample_id_normal\nsex: female\nsnv_vcf: oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz\nsv_vcf: oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz\nbam_tumor: oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam\nbai_tumor: oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai\nbam_normal: oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam\nbai_normal: oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + } ], - "timestamp": "2026-07-06T15:00:57.203386", + "timestamp": "2026-07-06T16:45:24.231416", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 589b6cc0440df12d9fe339e2d0ad94fed72fcac5 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 16:57:43 +0200 Subject: [PATCH 073/102] Update default test snapshot. --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 00830d6..12836cd 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -409,10 +409,10 @@ "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - "oncorefiner_params.yaml:md5,28d103d129e8e5d8ea672a7f7186d9d8" + "oncorefiner_params.yaml:md5,b111aa8543e1e0253c66ab5bd0d1b795" ] ], - "timestamp": "2026-07-06T15:47:38.825724", + "timestamp": "2026-07-06T16:52:49.957411", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 134607ae3323920bd7d2e70530168f991661a63e Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:00:28 +0200 Subject: [PATCH 074/102] Rename oncoanalyser_config. --- docs/parameters.md | 2 +- main.nf | 14 +++++++------- nextflow.config | 2 +- nextflow_schema.json | 2 +- workflows/oncoflow.nf | 12 ++++++------ 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index dde6322..c8d1fda 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -8,7 +8,7 @@ Necessary input files and nextflow options for running nf-core/oncoanlyser. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| -| `oncoanalyser_additional_config` | Path to additional config file for nf-core/oncoanlyser (optional). | `string` | | | | +| `oncoanalyser_config` | Path to additional config file for nf-core/oncoanlyser (optional). | `string` | | | | | `oncoanalyser_nextflow_opts` | Nextflow options for running nf-core/oncoanlyser. | `string` | | True | | | `oncoanalyser_params_file` | Path to params file for nf-core/oncoanlyser. | `string` | | | | | `oncoanalyser_samplesheet` | Path to csv samplesheet file for nf-core/oncoanalyser. | `string` | | | | diff --git a/main.nf b/main.nf index 39677a8..b40ff7c 100644 --- a/main.nf +++ b/main.nf @@ -27,11 +27,11 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: - val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline - val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline - val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline - val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - outdir // string: [mandatory] The output directory where the results will be saved + val_oncoanalyser_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -39,7 +39,7 @@ workflow CLINICALGENOMICS_ONCOFLOW { // WORKFLOW: Run pipeline // ONCOFLOW ( - val_oncoanalyser_additional_config, + val_oncoanalyser_config, val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, @@ -76,7 +76,7 @@ workflow { // WORKFLOW: Run main workflow // CLINICALGENOMICS_ONCOFLOW ( - params.oncoanalyser_additional_config, + params.oncoanalyser_config, params.oncoanalyser_nextflow_opts, params.oncoanalyser_params_file, params.oncoanalyser_samplesheet, diff --git a/nextflow.config b/nextflow.config index 2b37708..ce32a28 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,7 +10,7 @@ params { // Oncoanalyser input parameters - oncoanalyser_additional_config = '' + oncoanalyser_config = '' oncoanalyser_nextflow_opts = '' oncoanalyser_params_file = '' oncoanalyser_samplesheet = '' diff --git a/nextflow_schema.json b/nextflow_schema.json index d38ffe8..465de6f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -11,7 +11,7 @@ "description": "Necessary input files and nextflow options for running nf-core/oncoanlyser.", "default": "", "properties": { - "oncoanalyser_additional_config": { + "oncoanalyser_config": { "type": "string", "description": "Path to additional config file for nf-core/oncoanlyser (optional).", "format": "file-path", diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 1f56b2b..926cc37 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -15,11 +15,11 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: - val_oncoanalyser_additional_config // string: [optional] Additional config file for oncoanalyser pipeline - val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline - val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline - val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline - outdir // string: [mandatory] The output directory where the results will be saved + val_oncoanalyser_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -30,7 +30,7 @@ workflow ONCOFLOW { val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, - val_oncoanalyser_additional_config, + val_oncoanalyser_config, workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), ) From b6d09f8da57a1b0f46857ea1eb3833a0f34cfdbe Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:01:08 +0200 Subject: [PATCH 075/102] Update oncoanalyser_config description. --- docs/parameters.md | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index c8d1fda..33f7507 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -8,7 +8,7 @@ Necessary input files and nextflow options for running nf-core/oncoanlyser. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| -| `oncoanalyser_config` | Path to additional config file for nf-core/oncoanlyser (optional). | `string` | | | | +| `oncoanalyser_config` | Path to config file for nf-core/oncoanlyser (optional). | `string` | | | | | `oncoanalyser_nextflow_opts` | Nextflow options for running nf-core/oncoanlyser. | `string` | | True | | | `oncoanalyser_params_file` | Path to params file for nf-core/oncoanlyser. | `string` | | | | | `oncoanalyser_samplesheet` | Path to csv samplesheet file for nf-core/oncoanalyser. | `string` | | | | diff --git a/nextflow_schema.json b/nextflow_schema.json index 465de6f..5f8dae3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -13,7 +13,7 @@ "properties": { "oncoanalyser_config": { "type": "string", - "description": "Path to additional config file for nf-core/oncoanlyser (optional).", + "description": "Path to config file for nf-core/oncoanlyser (optional).", "format": "file-path", "exists": true, "fa_icon": "far fa-file" From e329f1a0fec32e0309c57742a5a17d9b7194862c Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Mon, 6 Jul 2026 17:01:41 +0200 Subject: [PATCH 076/102] Apply suggestion from @fellen31 Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- tests/default.nf.test | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index ae0c517..e83b72c 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', '**/pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assert workflow.success assertAll( { assert snapshot( From 5ca66c9525126da05f3580e5f7fed090f88339b9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:02:29 +0200 Subject: [PATCH 077/102] Harshil alignment in oncoflow.nf --- workflows/oncoflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 926cc37..82e74a9 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From f491a3f637471ff834cf32318eb9a3d547ef1488 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Mon, 6 Jul 2026 17:03:02 +0200 Subject: [PATCH 078/102] Apply suggestion from @fellen31 Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- workflows/oncoflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 82e74a9..b101c41 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -65,7 +65,7 @@ workflow ONCOFLOW { emit: oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] - versions = ch_versions // channel: [ path(versions.yml) ] + versions = ch_versions // channel: [path(versions.yml)] } /* From dd8490a97951a2fc5b37645c7e9e9e5bbc0273ef Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:03:45 +0200 Subject: [PATCH 079/102] Harshil alignment in nextflow.config --- nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index ce32a28..72c8dfa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,10 +10,10 @@ params { // Oncoanalyser input parameters - oncoanalyser_config = '' - oncoanalyser_nextflow_opts = '' - oncoanalyser_params_file = '' - oncoanalyser_samplesheet = '' + oncoanalyser_config = '' + oncoanalyser_nextflow_opts = '' + oncoanalyser_params_file = '' + oncoanalyser_samplesheet = '' // Boilerplate options outdir = null From d5ff51d0cba20f446e4f5d6ab1a3024866258ae6 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:06:44 +0200 Subject: [PATCH 080/102] Add pattern for oncoanalyser_params_file. --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5f8dae3..946a580 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -27,6 +27,7 @@ "type": "string", "description": "Path to params file for nf-core/oncoanlyser.", "format": "file-path", + "pattern": "^\\S+\\.(json|ya?ml)$", "exists": true, "fa_icon": "fas fa-file" }, From f73a519d8c68cb783911f0f96a09a7e548558ee0 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 6 Jul 2026 17:13:42 +0200 Subject: [PATCH 081/102] Simplify ignore statements in default test and nftignore. Update snapshot. --- tests/.nftignore | 3 +-- tests/default.nf.test | 2 +- tests/default.nf.test.snap | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 622332c..10d08cd 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,6 +1,5 @@ .DS_Store -pipeline_info/*.{html,json,txt,yml} -**/pipeline_info/*.{html,json,txt,yml} +**pipeline_info/*.{html,json,txt,yml} **/multiqc/** oncoanalyser/**/*.gz oncoanalyser/**/*.command.* diff --git a/tests/default.nf.test b/tests/default.nf.test index e83b72c..eb4ac23 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -14,7 +14,7 @@ nextflow_pipeline { then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', '**/pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['**pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b8077b8..136ffd6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -409,7 +409,7 @@ "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-07-06T10:35:01.939539", + "timestamp": "2026-07-06T17:11:10.792699", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 8740f948f09cae9be3e2f550b8e1ddaebc888301 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 09:21:25 +0200 Subject: [PATCH 082/102] Update module test and snapshot. --- .../tests/main.nf.test | 11 +++-- .../tests/main.nf.test.snap | 41 +++++++++---------- 2 files changed, 27 insertions(+), 25 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index 1332e91..98e5736 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -20,16 +20,21 @@ nextflow_process { input[3] = "test_sample_id_normal" input[4] = "female" input[5] = "$projectDir" - input[6] = "test_outdir" + input[6] = "$outputDir" """ } } then { + // Remove the outputDir from the params file content as it changes every run and therefore cannot be snapshot + def params_file = file(process.out.params_file[0]) + def clean_params_file_content = params_file.text.replace("$outputDir", "") + assert process.success assertAll( { assert snapshot( - process.out + process.out.versions_createoncorefinerparamsfile, + clean_params_file_content.split("\n") ).match() } ) } @@ -49,7 +54,7 @@ nextflow_process { input[3] = "test_sample_id_normal" input[4] = "female" input[5] = "$projectDir" - input[6] = "test_outdir" + input[6] = "$outputDir" """ } } diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap index e3b14aa..34d3be2 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -1,30 +1,27 @@ { "Given a valid oncoanalyser results directory": { "content": [ - { - "0": [ - "oncorefiner_params.yaml:md5,2f1b615720d5629714cf3e237faffa60" - ], - "1": [ - [ - "CREATE_ONCOREFINER_PARAMS_FILE", - "createoncorefinerparamsfile", - "1.0" - ] - ], - "params_file": [ - "oncorefiner_params.yaml:md5,2f1b615720d5629714cf3e237faffa60" - ], - "versions_createoncorefinerparamsfile": [ - [ - "CREATE_ONCOREFINER_PARAMS_FILE", - "createoncorefinerparamsfile", - "1.0" - ] + [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" ] - } + ], + [ + "case_id: test_case_id", + "sample_id_tumor: test_sample_id_tumor", + "sample_id_normal: test_sample_id_normal", + "sex: female", + "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", + "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", + "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam", + "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", + "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam", + "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + ] ], - "timestamp": "2026-07-06T16:45:24.231416", + "timestamp": "2026-07-07T09:19:21.656387", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 47ca313fd4c9b1764c4ce908d6cf93a614a57f4f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 09:25:34 +0200 Subject: [PATCH 083/102] Update changelog. --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce3b98b..6b5b3df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) Added `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_additional_config`, `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. +- [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` local module. +- [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added metadata parameters `case_id`, `sample_id_tumor`, `sample_id_normal`, `subject_id` and `sex`, necessary for creating the `oncoanalyser` params file using the `CREATE_ONCOREFINER_PARAMS_FILE` local module. ### `Changed` @@ -19,6 +21,7 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. +- [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` module to `ONCOFLOW` workflow. ### `Fixed` From a46f87d77b0ea5a78ffaecf140f73dc32fc37141 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 11:58:54 +0200 Subject: [PATCH 084/102] Fix " in params file generation. --- modules/local/createoncorefinerparamsfile/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf index c47b645..9e18b2e 100644 --- a/modules/local/createoncorefinerparamsfile/main.nf +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -34,7 +34,7 @@ process CREATE_ONCOREFINER_PARAMS_FILE { def oncorefiner_params_file = [ - "\"case_id: ${case_id}", + "case_id: ${case_id}", "sample_id_tumor: ${sample_id_tumor}", "sample_id_normal: ${sample_id_normal}", "sex: ${sex}", @@ -43,13 +43,13 @@ process CREATE_ONCOREFINER_PARAMS_FILE { "bam_tumor: ${path_bam_tumor}", "bai_tumor: ${path_bai_tumor}", "bam_normal: ${path_bam_normal}", - "bai_normal: ${path_bai_normal}\"" + "bai_normal: ${path_bai_normal}" ].join("\\n") """ echo $args - printf $oncorefiner_params_file > oncorefiner_params.yaml + printf "$oncorefiner_params_file" > oncorefiner_params.yaml """ stub: From 955fb5f3d2c99ce4cdcd9b6b987a64c2bd5b9693 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Tue, 7 Jul 2026 12:03:32 +0200 Subject: [PATCH 085/102] Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- modules/local/createoncorefinerparamsfile/meta.yml | 1 - modules/local/createoncorefinerparamsfile/tests/main.nf.test | 2 -- 2 files changed, 3 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/meta.yml b/modules/local/createoncorefinerparamsfile/meta.yml index d2b97e6..e8f6cd2 100644 --- a/modules/local/createoncorefinerparamsfile/meta.yml +++ b/modules/local/createoncorefinerparamsfile/meta.yml @@ -1,5 +1,4 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -# # TODO nf-core: Add a description of the module and list keywords name: "createoncorefinerparamsfile" description: write your description here keywords: diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index 98e5736..75d9391 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -1,5 +1,3 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test createoncorefinerparamsfile nextflow_process { name "Test Process CREATE_ONCOREFINER_PARAMS_FILE" From ab378c5f5ed52c8e4f87c9900c8feefe2cc3f42d Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 12:05:41 +0200 Subject: [PATCH 086/102] Update test to replace "" --- .../createoncorefinerparamsfile/tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index 75d9391..d3b81dd 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -26,7 +26,7 @@ nextflow_process { then { // Remove the outputDir from the params file content as it changes every run and therefore cannot be snapshot def params_file = file(process.out.params_file[0]) - def clean_params_file_content = params_file.text.replace("$outputDir", "") + def clean_params_file_content = params_file.text.replace("$outputDir", "") assert process.success assertAll( diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap index 34d3be2..fe18c3e 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -13,15 +13,15 @@ "sample_id_tumor: test_sample_id_tumor", "sample_id_normal: test_sample_id_normal", "sex: female", - "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", - "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", - "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam", - "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", - "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam", - "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", + "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", + "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam", + "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", + "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam", + "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-07T09:19:21.656387", + "timestamp": "2026-07-07T12:05:07.570191", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 59e6c780737ef6d64e8424b8f341ff7b15b7aa89 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 12:51:06 +0200 Subject: [PATCH 087/102] Adjust default test to snapshot params file contente --- .../tests/main.nf.test | 2 +- tests/default.nf.test | 12 ++++++++++-- tests/default.nf.test.snap | 17 ++++++++++++++--- 3 files changed, 25 insertions(+), 6 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index d3b81dd..eae87c4 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { } then { - // Remove the outputDir from the params file content as it changes every run and therefore cannot be snapshot + // Remove the run $outputDir path from the params file content so it can be snapshot def params_file = file(process.out.params_file[0]) def clean_params_file_content = params_file.text.replace("$outputDir", "") diff --git a/tests/default.nf.test b/tests/default.nf.test index eb4ac23..68c6681 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -16,7 +16,13 @@ nextflow_pipeline { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['**pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content - def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['oncorefiner/oncorefiner_params.yaml']) + + // Remove the run $outputDir path from the params file content so it can be snapshot + def oncorefiner_params_file_path = "$outputDir/oncorefiner/oncorefiner_params.yaml" + def params_file = file(oncorefiner_params_file_path) + def clean_params_file_content = params_file.text.replace("$outputDir", "") + assert workflow.success assertAll( { assert snapshot( @@ -25,7 +31,9 @@ nextflow_pipeline { // All stable path name, with a relative path stable_path, // All files with stable contents - stable_content + stable_content, + // Oncorefiner params file without the $outputDir path + clean_params_file_content.split("\n") ).match() } ) } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 12836cd..42b6c22 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -408,11 +408,22 @@ "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - "oncorefiner_params.yaml:md5,b111aa8543e1e0253c66ab5bd0d1b795" + "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "case_id: test_case_id", + "sample_id_tumor: test_sample_id_tumor", + "sample_id_normal: test_sample_id_normal", + "sex: female", + "snv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "sv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "bam_tumor: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_tumor.normal.redux.bam", + "bai_tumor: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", + "bam_normal: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_normal.normal.redux.bam", + "bai_normal: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-06T16:52:49.957411", + "timestamp": "2026-07-07T12:45:31.962618", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From b465cb6f2226a273435217f55fb628077a60e581 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 12:54:23 +0200 Subject: [PATCH 088/102] Remove ext.args from module. --- .../local/createoncorefinerparamsfile/main.nf | 32 +++++++------------ 1 file changed, 12 insertions(+), 20 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf index 9e18b2e..bf96099 100644 --- a/modules/local/createoncorefinerparamsfile/main.nf +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -21,16 +21,14 @@ process CREATE_ONCOREFINER_PARAMS_FILE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def oncoanalyser_output_dir = file(outdir).resolve("oncoanalyser/${oncoanalyser_results_dir}") - def path_snv_vcf = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") - def path_sv_vcf = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") - def path_bam_tumor = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") - def path_bai_tumor = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") - def path_bam_normal = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") - def path_bai_normal = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") + def snv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") + def sv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") + def bam_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") + def bai_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") + def bam_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") + def bai_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") def oncorefiner_params_file = [ @@ -38,26 +36,20 @@ process CREATE_ONCOREFINER_PARAMS_FILE { "sample_id_tumor: ${sample_id_tumor}", "sample_id_normal: ${sample_id_normal}", "sex: ${sex}", - "snv_vcf: ${path_snv_vcf}", - "sv_vcf: ${path_sv_vcf}", - "bam_tumor: ${path_bam_tumor}", - "bai_tumor: ${path_bai_tumor}", - "bam_normal: ${path_bam_normal}", - "bai_normal: ${path_bai_normal}" + "snv_vcf: ${snv_vcf_path}", + "sv_vcf: ${sv_vcf_path}", + "bam_tumor: ${bam_tumor_path}", + "bai_tumor: ${bai_tumor_path}", + "bam_normal: ${bam_normal_path}", + "bai_normal: ${bai_normal_path}" ].join("\\n") """ - echo $args - printf "$oncorefiner_params_file" > oncorefiner_params.yaml """ stub: - def args = task.ext.args ?: '' - """ - echo $args - touch oncorefiner_params.yaml """ } From f9a9bb0136e7838183f40bb3db9ccfe242e6abc9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 13:01:11 +0200 Subject: [PATCH 089/102] update variable names oncorefiner_params_file --- .../local/createoncorefinerparamsfile/tests/main.nf.test | 6 +++--- tests/default.nf.test | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index eae87c4..1d3943e 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -25,14 +25,14 @@ nextflow_process { then { // Remove the run $outputDir path from the params file content so it can be snapshot - def params_file = file(process.out.params_file[0]) - def clean_params_file_content = params_file.text.replace("$outputDir", "") + def oncorefiner_params_file = file(process.out.params_file[0]) + def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replace("$outputDir", "") assert process.success assertAll( { assert snapshot( process.out.versions_createoncorefinerparamsfile, - clean_params_file_content.split("\n") + clean_oncorefiner_params_file_content.split("\n") ).match() } ) } diff --git a/tests/default.nf.test b/tests/default.nf.test index 68c6681..04045c1 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { // Remove the run $outputDir path from the params file content so it can be snapshot def oncorefiner_params_file_path = "$outputDir/oncorefiner/oncorefiner_params.yaml" - def params_file = file(oncorefiner_params_file_path) - def clean_params_file_content = params_file.text.replace("$outputDir", "") + def oncorefiner_params_file = file(oncorefiner_params_file_path) + def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replace("$outputDir", "") assert workflow.success assertAll( @@ -33,7 +33,7 @@ nextflow_pipeline { // All files with stable contents stable_content, // Oncorefiner params file without the $outputDir path - clean_params_file_content.split("\n") + clean_oncorefiner_params_file_content.split("\n") ).match() } ) } From 0ac04d65747ea8b634154d94346a676995c35255 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 13:17:02 +0200 Subject: [PATCH 090/102] Correct meta.yml --- modules/local/createoncorefinerparamsfile/meta.yml | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/meta.yml b/modules/local/createoncorefinerparamsfile/meta.yml index e8f6cd2..f158896 100644 --- a/modules/local/createoncorefinerparamsfile/meta.yml +++ b/modules/local/createoncorefinerparamsfile/meta.yml @@ -1,19 +1,10 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "createoncorefinerparamsfile" -description: write your description here +description: Generate a parameters file for the oncorefiner pipeline based on the output of the oncoanalyser pipeline. keywords: - samplesheet - oncoanalyser - oncorefiner -tools: - - "createoncorefinerparamsfile": - description: "Generate a parameters file for the oncorefiner pipeline based on the output of the oncoanalyser pipeline." - homepage: "" - documentation: "" - tool_dev_url: "" - doi: "" - licence: null - identifier: null input: - case_id: @@ -34,6 +25,9 @@ input: - oncoanalyser_results_dir: type: directory description: Path to the output directory of the oncoanalyser pipeline + - outdir: + type: string + description: Output directory for pipeline output files output: parameters_file: - "oncorefiner_params.yaml": From 6ca45a9d820cc09ff277594685a71124061fa787 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Tue, 7 Jul 2026 13:20:19 +0200 Subject: [PATCH 091/102] feat: Add `NFCORE_ONCOANALYSER` to main workflow (#3) ### Added - `NFCORE_ONCOANALYSER` module using `NEXTFLOW_RUN` to main workflow. - Input parameters for running `oncoanalyser`: - `oncoanalyser_config` - `oncoanalyser_nextflow_opts` - `oncoanalyser_params_file` - `oncoanalyser_samplesheet` ### Changed - Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. - Changed default test to not capture `pipeline_info` files for all pipelines. --- CHANGELOG.md | 11 +- conf/test.config | 9 +- docs/parameters.md | 11 + main.nf | 31 ++- nextflow.config | 6 + nextflow_schema.json | 42 ++++ tests/.nftignore | 5 +- tests/default.nf.test | 4 +- tests/default.nf.test.snap | 418 +++++++++++++++++++++++++++++++++++++ workflows/oncoflow.nf | 22 +- 10 files changed, 542 insertions(+), 17 deletions(-) create mode 100644 tests/default.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index e8e704c..5025be0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,16 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` -- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. +- [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) Added `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_config`, `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. + +### `Changed` + +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. ### `Fixed` diff --git a/conf/test.config b/conf/test.config index 74c7407..b721785 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,11 +19,8 @@ process { } params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + config_profile_name = 'Test profile (stub runs for all pipelines)' + config_profile_description = 'Minimal test where all pipelines are run in stub mode to check that pipelines are run sequentially' - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' } diff --git a/docs/parameters.md b/docs/parameters.md index 3892a92..33f7507 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -2,6 +2,17 @@ Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow. +## Oncoanalyser + +Necessary input files and nextflow options for running nf-core/oncoanlyser. + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `oncoanalyser_config` | Path to config file for nf-core/oncoanlyser (optional). | `string` | | | | +| `oncoanalyser_nextflow_opts` | Nextflow options for running nf-core/oncoanlyser. | `string` | | True | | +| `oncoanalyser_params_file` | Path to params file for nf-core/oncoanlyser. | `string` | | | | +| `oncoanalyser_samplesheet` | Path to csv samplesheet file for nf-core/oncoanalyser. | `string` | | | | + ## Input/output options Define where the pipeline should find input data and save output data. diff --git a/main.nf b/main.nf index fb25380..7232b7c 100644 --- a/main.nf +++ b/main.nf @@ -12,8 +12,7 @@ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { ONCOFLOW } from './workflows/oncoflow' +include { ONCOFLOW } from './workflows/oncoflow' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_oncoflow_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_oncoflow_pipeline' /* @@ -28,7 +27,11 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_onco workflow CLINICALGENOMICS_ONCOFLOW { take: - outdir // string: The output directory where the results will be saved + val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: @@ -36,8 +39,15 @@ workflow CLINICALGENOMICS_ONCOFLOW { // WORKFLOW: Run pipeline // ONCOFLOW ( - outdir, + val_oncoanalyser_config, + val_oncoanalyser_nextflow_opts, + val_oncoanalyser_params_file, + val_oncoanalyser_samplesheet, + outdir ) + + emit: + oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(oncoanalyser_output_directory)] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -66,6 +76,10 @@ workflow { // WORKFLOW: Run main workflow // CLINICALGENOMICS_ONCOFLOW ( + params.oncoanalyser_config, + params.oncoanalyser_nextflow_opts, + params.oncoanalyser_params_file, + params.oncoanalyser_samplesheet, params.outdir ) @@ -79,6 +93,15 @@ workflow { params.outdir, params.monochrome_logs, ) + + publish: + oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.out.oncoanalyser_output +} + +output { + oncoanalyser_output { + path "oncoanalyser" + } } /* diff --git a/nextflow.config b/nextflow.config index 3b2582e..72c8dfa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,6 +9,12 @@ // Global default params, used in configs params { + // Oncoanalyser input parameters + oncoanalyser_config = '' + oncoanalyser_nextflow_opts = '' + oncoanalyser_params_file = '' + oncoanalyser_samplesheet = '' + // Boilerplate options outdir = null publish_dir_mode = 'copy' diff --git a/nextflow_schema.json b/nextflow_schema.json index dfbfead..946a580 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -5,6 +5,45 @@ "description": "Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow.", "type": "object", "$defs": { + "oncoanalyser": { + "title": "Oncoanalyser", + "type": "object", + "description": "Necessary input files and nextflow options for running nf-core/oncoanlyser.", + "default": "", + "properties": { + "oncoanalyser_config": { + "type": "string", + "description": "Path to config file for nf-core/oncoanlyser (optional).", + "format": "file-path", + "exists": true, + "fa_icon": "far fa-file" + }, + "oncoanalyser_nextflow_opts": { + "type": "string", + "description": "Nextflow options for running nf-core/oncoanlyser.", + "fa_icon": "fas fa-terminal" + }, + "oncoanalyser_params_file": { + "type": "string", + "description": "Path to params file for nf-core/oncoanlyser.", + "format": "file-path", + "pattern": "^\\S+\\.(json|ya?ml)$", + "exists": true, + "fa_icon": "fas fa-file" + }, + "oncoanalyser_samplesheet": { + "type": "string", + "description": "Path to csv samplesheet file for nf-core/oncoanalyser.", + "format": "file-path", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "exists": true, + "fa_icon": "fas fa-file-csv" + } + }, + "required": ["oncoanalyser_nextflow_opts"], + "fa_icon": "fas fa-file-import" + }, "input_output_options": { "title": "Input/output options", "type": "object", @@ -153,6 +192,9 @@ } }, "allOf": [ + { + "$ref": "#/$defs/oncoanalyser" + }, { "$ref": "#/$defs/input_output_options" }, diff --git a/tests/.nftignore b/tests/.nftignore index 73eb92f..10d08cd 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,2 +1,5 @@ .DS_Store -pipeline_info/*.{html,json,txt,yml} +**pipeline_info/*.{html,json,txt,yml} +**/multiqc/** +oncoanalyser/**/*.gz +oncoanalyser/**/*.command.* diff --git a/tests/default.nf.test b/tests/default.nf.test index 4e6c99f..eb4ac23 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" - test("-profile test") { + test("-profile test (stub runs for all pipelines)") { when { params { @@ -14,7 +14,7 @@ nextflow_pipeline { then { // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) - def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['**pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..136ffd6 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,418 @@ +{ + "-profile test (stub runs for all pipelines)": { + "content": [ + null, + [ + "oncoanalyser", + "oncoanalyser/results", + "oncoanalyser/results/pipeline_info", + "oncoanalyser/results/pipeline_info/software_versions.yml", + "oncoanalyser/results/subject_a", + "oncoanalyser/results/subject_a/alignments", + "oncoanalyser/results/subject_a/alignments/dna", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.duplicate_freq.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.jitter_params.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.ms_table.tsv.gz", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.duplicate_freq.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.jitter_params.tsv", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.ms_table.tsv.gz", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam", + "oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam.bai", + "oncoanalyser/results/subject_a/amber", + "oncoanalyser/results/subject_a/amber/placeholder", + "oncoanalyser/results/subject_a/bamtools", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/chord", + "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv", + "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.prediction.tsv", + "oncoanalyser/results/subject_a/cider", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.locus_stats.tsv", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", + "oncoanalyser/results/subject_a/cobalt", + "oncoanalyser/results/subject_a/cobalt/placeholder", + "oncoanalyser/results/subject_a/cuppa", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.pred_summ.tsv", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.vis.png", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa.vis_data.tsv", + "oncoanalyser/results/subject_a/cuppa/subject_a.tumor.cuppa_data.tsv.gz", + "oncoanalyser/results/subject_a/esvee", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz", + "oncoanalyser/results/subject_a/esvee/subject_a.tumor.esvee.unfiltered.vcf.gz.tbi", + "oncoanalyser/results/subject_a/isofox", + "oncoanalyser/results/subject_a/isofox/placeholder", + "oncoanalyser/results/subject_a/lilac", + "oncoanalyser/results/subject_a/lilac/placeholder", + "oncoanalyser/results/subject_a/linx", + "oncoanalyser/results/subject_a/linx/germline_annotations", + "oncoanalyser/results/subject_a/linx/germline_annotations/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_annotations", + "oncoanalyser/results/subject_a/linx/somatic_annotations/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_plots", + "oncoanalyser/results/subject_a/linx/somatic_plots/all", + "oncoanalyser/results/subject_a/linx/somatic_plots/all/placeholder", + "oncoanalyser/results/subject_a/linx/somatic_plots/reportable", + "oncoanalyser/results/subject_a/linx/somatic_plots/reportable/placeholder", + "oncoanalyser/results/subject_a/linx/subject_a.tumor_linx.html", + "oncoanalyser/results/subject_a/logs", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.amber.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.chord.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.cobalt.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.cuppa.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.esvee.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.isofox.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.lilac.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linx_visualiser.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.linxreport.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_annotate_fusions.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_finder.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.neo_scorer.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.orange.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.pave_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.pave_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.peach.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.purple.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_append_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_germline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sage_somatic.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.sigs.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.teal_pipeline.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.teal_prep.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.virusbreakend.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.err", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.log", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.out", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.run", + "oncoanalyser/results/subject_a/logs/subject_a.virusinterpreter.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.bamtools.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.normal.redux.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.bamtools.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.cider.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor.redux.command.sh", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.err", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.log", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.out", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.run", + "oncoanalyser/results/subject_a/logs/subject_a_subject_a.tumor_rna.cider.command.sh", + "oncoanalyser/results/subject_a/neo", + "oncoanalyser/results/subject_a/neo/annotated_fusions", + "oncoanalyser/results/subject_a/neo/annotated_fusions/subject_a.tumor.isf.neoepitope.tsv", + "oncoanalyser/results/subject_a/neo/finder", + "oncoanalyser/results/subject_a/neo/scorer", + "oncoanalyser/results/subject_a/orange", + "oncoanalyser/results/subject_a/orange/subject_a.tumor.orange.json", + "oncoanalyser/results/subject_a/orange/subject_a.tumor.orange.pdf", + "oncoanalyser/results/subject_a/pave", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz", + "oncoanalyser/results/subject_a/pave/subject_a.tumor.pave.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/peach", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.events.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.gene.events.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.haplotypes.all.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.haplotypes.best.tsv", + "oncoanalyser/results/subject_a/peach/subject_a.normal.peach.qc.tsv", + "oncoanalyser/results/subject_a/purple", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.cnv.gene.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.cnv.somatic.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.germline.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.somatic.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.purity.tsv", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.qc", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", + "oncoanalyser/results/subject_a/sage", + "oncoanalyser/results/subject_a/sage/germline", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", + "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage/somatic", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append", + "oncoanalyser/results/subject_a/sage_append/germline", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.sage.append.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal_query.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_append/somatic", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.frag_lengths.tsv.gz", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor_query.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sigs", + "oncoanalyser/results/subject_a/sigs/placeholder", + "oncoanalyser/results/subject_a/teal", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.telbam.bam", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.telbam.bam.bai", + "oncoanalyser/results/subject_a/teal/subject_a.normal.teal.{tellength.tsv}", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.breakend.tsv.gz", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.telbam.bam", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.telbam.bam.bai", + "oncoanalyser/results/subject_a/teal/subject_a.tumor.teal.tellength.tsv", + "oncoanalyser/results/subject_a/virusbreakend", + "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.summary.tsv", + "oncoanalyser/results/subject_a/virusbreakend/subject_a.tumor.virusbreakend.vcf", + "oncoanalyser/results/subject_a/virusinterpreter", + "oncoanalyser/results/subject_a/virusinterpreter/subject_a.tumor.virus.annotated.tsv", + "pipeline_info", + "pipeline_info/oncoflow_software_versions.yml" + ], + [ + "subject_a.normal.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.duplicate_freq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.jitter_params.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.redux.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.redux.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.flag_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.frag_length.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.partition_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.bam_metric.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.flag_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.frag_length.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.partition_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.bam_metric.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.chord.mutation_contexts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.chord.prediction.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_rna.cider.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_rna.cider.locus_stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.pred_summ.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.vis.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.cuppa.vis_data.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.esvee.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.esvee.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.esvee.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_linx.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.isf.neoepitope.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.orange.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.orange.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.pave.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.pave.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.gene.events.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.haplotypes.all.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.haplotypes.best.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.peach.qc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.cnv.gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.cnv.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.driver.catalog.germline.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.driver.catalog.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.purity.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.qc:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.teal.{tellength.tsv}:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "timestamp": "2026-07-06T17:11:10.792699", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 80e8f86..fb19aa3 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -3,7 +3,8 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -14,12 +15,25 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi workflow ONCOFLOW { take: - outdir + val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline + val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline + val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline + val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + outdir // string: [mandatory] The output directory where the results will be saved main: def ch_versions = channel.empty() + NFCORE_ONCOANALYSER( + 'nf-core/oncoanalyser', + val_oncoanalyser_nextflow_opts, + val_oncoanalyser_params_file, + val_oncoanalyser_samplesheet, + val_oncoanalyser_config, + workflow.workDir.resolve('nf-core/oncoanalyser').toUriString(), + ) + // // Collate and save software versions // @@ -48,8 +62,10 @@ workflow ONCOFLOW { sort: true, newLine: true ) + emit: - versions = ch_versions // channel: [ path(versions.yml) ] + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] + versions = ch_versions // channel: [path(versions.yml)] } /* From 43ca4cc2258e711c4a121bb550ae10df94bba715 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Tue, 7 Jul 2026 15:56:10 +0200 Subject: [PATCH 092/102] fix: Address review comments for `add-create-oncorefiner-params-file` (#6) ### Changed - Update test comment related to `clean_oncorefiner_params_file_content`. --- modules/local/createoncorefinerparamsfile/tests/main.nf.test | 2 +- tests/default.nf.test | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index 1d3943e..036bd7b 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { } then { - // Remove the run $outputDir path from the params file content so it can be snapshot + // The oncorefiner params file contains $outputDir (includes the full path to the nf-test work directory), which varies for every test run def oncorefiner_params_file = file(process.out.params_file[0]) def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replace("$outputDir", "") diff --git a/tests/default.nf.test b/tests/default.nf.test index 04045c1..b6a15e0 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['oncorefiner/oncorefiner_params.yaml']) - // Remove the run $outputDir path from the params file content so it can be snapshot + // The oncorefiner params file contains $outputDir (includes the full path to the nf-test work directory), which varies for every test run def oncorefiner_params_file_path = "$outputDir/oncorefiner/oncorefiner_params.yaml" def oncorefiner_params_file = file(oncorefiner_params_file_path) def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replace("$outputDir", "") @@ -32,7 +32,7 @@ nextflow_pipeline { stable_path, // All files with stable contents stable_content, - // Oncorefiner params file without the $outputDir path + // Oncorefiner params file without the run $outputDir path clean_oncorefiner_params_file_content.split("\n") ).match() } ) From b5dc5659c4b70593b0ec3793f8184c603d77ad55 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 16:01:52 +0200 Subject: [PATCH 093/102] Fix bug with incorrect `snv_vcf_path` and `sv_vcf_path`. --- modules/local/createoncorefinerparamsfile/main.nf | 8 ++++---- .../tests/main.nf.test.snap | 10 +++++----- tests/default.nf.test.snap | 10 +++++----- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf index bf96099..a057289 100644 --- a/modules/local/createoncorefinerparamsfile/main.nf +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -25,10 +25,10 @@ process CREATE_ONCOREFINER_PARAMS_FILE { def snv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") def sv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") - def bam_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam") - def bai_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_tumor}.normal.redux.bam.bai") - def bam_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam") - def bai_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${sample_id_normal}.normal.redux.bam.bai") + def bam_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam") + def bai_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam.bai") + def bam_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam") + def bai_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam.bai") def oncorefiner_params_file = [ diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap index fe18c3e..eccb8bb 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -15,13 +15,13 @@ "sex: female", "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", - "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam", - "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", - "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam", - "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam", + "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam.bai", + "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam", + "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-07T12:05:07.570191", + "timestamp": "2026-07-07T15:42:48.686446", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 42b6c22..3faaafa 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -417,13 +417,13 @@ "sex: female", "snv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", "sv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "bam_tumor: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_tumor.normal.redux.bam", - "bai_tumor: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_tumor.normal.redux.bam.bai", - "bam_normal: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_normal.normal.redux.bam", - "bai_normal: /oncoanalyser/results/subject_a/alignments/dna/test_sample_id_normal.normal.redux.bam.bai" + "bam_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", + "bai_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai", + "bam_normal: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", + "bai_normal: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-07T12:45:31.962618", + "timestamp": "2026-07-07T15:56:59.927545", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 8cab2ce0a1fa3e6865ce3d24ac1b5f31eae8ba7b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 16:08:44 +0200 Subject: [PATCH 094/102] Remove Additonal from info string. --- main.nf | 2 +- workflows/oncoflow.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 5bbab88..c3a97ec 100644 --- a/main.nf +++ b/main.nf @@ -28,7 +28,7 @@ workflow CLINICALGENOMICS_ONCOFLOW { take: val_case_id // string: [mandatory] Case ID - val_oncoanalyser_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 2106a6a..661464b 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -17,7 +17,7 @@ workflow ONCOFLOW { take: val_case_id // string: [mandatory] Case ID - val_oncoanalyser_config // string: [optional] Additional config file for oncoanalyser pipeline + val_oncoanalyser_config // string: [optional] Config file for oncoanalyser pipeline val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline From 209a6c190785747650b2ceed650a86b2b888d88b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 16:15:29 +0200 Subject: [PATCH 095/102] Correct order in changelog. --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 97c5057..da2899e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,10 +17,10 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Changed` +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` module to `ONCOFLOW` workflow. ### `Fixed` From 4a1f2dc73e538d9b4a913111cea2b91bd90f9dfb Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 7 Jul 2026 16:18:44 +0200 Subject: [PATCH 096/102] Corrext changelog. --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index da2899e..39a77d9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,10 +10,11 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: ### `Added` - [#2](https://github.com/Clinical-Genomics/oncoflow/pull/2) Added `NEXTFLOW_RUN` local module based on `mahesh-panchal/nf-cascade`. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added `NFCORE_ONCOANALYSER` using the `NEXTFLOW_RUN` local module to run the `nf-core/oncoanalyser` pipeline in `ONCOFLOW` workflow. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Added input parameters for running `nf-core/oncoanalyser`: `oncoanalyser_config`, `oncoanalyser_nextflow_opts`, `oncoanalyser_params_file` and `oncoanalyser_samplesheet`. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` local module. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added metadata parameters `case_id`, `sample_id_tumor`, `sample_id_normal`, `subject_id` and `sex`, necessary for creating the `oncoanalyser` params file using the `CREATE_ONCOREFINER_PARAMS_FILE` local module. +- [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` module to `ONCOFLOW` workflow. ### `Changed` @@ -21,7 +22,6 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. -- [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` module to `ONCOFLOW` workflow. ### `Fixed` From a09f2d74b239e5021ab97e4f041ddf5eb6e62a41 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Wed, 8 Jul 2026 15:57:46 +0200 Subject: [PATCH 097/102] fix: `CREATE_ONCOREFINER_PARAMS_FILE` to add support for tumor only analysis (#7) ### Fixed - `CREATE_ONCOREFINER_PARAMS_FILE` to: - add support for tumor only analysis. - fix bug in `bam/bai_tumor` file path. --- .../local/createoncorefinerparamsfile/main.nf | 8 +-- .../tests/main.nf.test | 62 +++++++++++++++- .../tests/main.nf.test.snap | 71 +++++++++++++++++-- tests/default.nf.test.snap | 4 +- 4 files changed, 131 insertions(+), 14 deletions(-) diff --git a/modules/local/createoncorefinerparamsfile/main.nf b/modules/local/createoncorefinerparamsfile/main.nf index a057289..0742121 100644 --- a/modules/local/createoncorefinerparamsfile/main.nf +++ b/modules/local/createoncorefinerparamsfile/main.nf @@ -25,10 +25,10 @@ process CREATE_ONCOREFINER_PARAMS_FILE { def snv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.somatic.vcf.gz") def sv_vcf_path = oncoanalyser_output_dir.resolve("${subject_id}/purple/${subject_id}.tumor.purple.sv.vcf.gz") - def bam_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam") - def bai_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam.bai") - def bam_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam") - def bai_normal_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam.bai") + def bam_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.tumor.redux.bam") + def bai_tumor_path = oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.tumor.redux.bam.bai") + def bam_normal_path = sample_id_normal ? oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam") : '' + def bai_normal_path = sample_id_normal ? oncoanalyser_output_dir.resolve("${subject_id}/alignments/dna/${subject_id}.normal.redux.bam.bai") : '' def oncorefiner_params_file = [ diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test b/modules/local/createoncorefinerparamsfile/tests/main.nf.test index 036bd7b..0feb2f4 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test @@ -7,7 +7,7 @@ nextflow_process { tag "modules" tag "create_oncorefiner_params_file" - test("Given a valid oncoanalyser results directory") { + test("Tumor Normal") { when { process { @@ -39,7 +39,7 @@ nextflow_process { } - test("-stub") { + test("Tumor Normal -stub") { options "-stub" @@ -66,4 +66,62 @@ nextflow_process { } + test("Tumor Only") { + + when { + process { + """ + input[0] = "test_case_id" + input[1] = "test_subject_id" + input[2] = "test_sample_id_tumor" + input[3] = "" + input[4] = "female" + input[5] = "$projectDir" + input[6] = "$outputDir" + """ + } + } + + then { + // The oncorefiner params file contains $outputDir (includes the full path to the nf-test work directory), which varies for every test run + def oncorefiner_params_file = file(process.out.params_file[0]) + def clean_oncorefiner_params_file_content = oncorefiner_params_file.text.replace("$outputDir", "") + + assert process.success + assertAll( + { assert snapshot( + process.out.versions_createoncorefinerparamsfile, + clean_oncorefiner_params_file_content.split("\n") + ).match() } + ) + } + + } + + test("Tumor Only -stub") { + + options "-stub" + + when { + process { + """ + input[0] = "test_case_id" + input[1] = "test_subject_id" + input[2] = "test_sample_id_tumor" + input[3] = "" + input[4] = "female" + input[5] = "$projectDir" + input[6] = "$outputDir" + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } } diff --git a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap index eccb8bb..efc9e58 100644 --- a/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap +++ b/modules/local/createoncorefinerparamsfile/tests/main.nf.test.snap @@ -1,5 +1,36 @@ { - "Given a valid oncoanalyser results directory": { + "Tumor Normal -stub": { + "content": [ + { + "0": [ + "oncorefiner_params.yaml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ], + "params_file": [ + "oncorefiner_params.yaml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions_createoncorefinerparamsfile": [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ] + } + ], + "timestamp": "2026-07-08T10:54:19.476191", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "Tumor Normal": { "content": [ [ [ @@ -15,19 +46,47 @@ "sex: female", "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", - "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam", - "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam.bai", + "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.tumor.redux.bam", + "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.tumor.redux.bam.bai", "bam_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam", "bai_normal: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-07T15:42:48.686446", + "timestamp": "2026-07-08T10:54:15.18238", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "Tumor Only": { + "content": [ + [ + [ + "CREATE_ONCOREFINER_PARAMS_FILE", + "createoncorefinerparamsfile", + "1.0" + ] + ], + [ + "case_id: test_case_id", + "sample_id_tumor: test_sample_id_tumor", + "sample_id_normal: ", + "sex: female", + "snv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.somatic.vcf.gz", + "sv_vcf: /oncoanalyser/oncoflow/test_subject_id/purple/test_subject_id.tumor.purple.sv.vcf.gz", + "bam_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.tumor.redux.bam", + "bai_tumor: /oncoanalyser/oncoflow/test_subject_id/alignments/dna/test_subject_id.tumor.redux.bam.bai", + "bam_normal: ", + "bai_normal: " + ] + ], + "timestamp": "2026-07-08T15:36:03.021214", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" } }, - "-stub": { + "Tumor Only -stub": { "content": [ { "0": [ @@ -52,7 +111,7 @@ ] } ], - "timestamp": "2026-07-06T14:09:16.928105", + "timestamp": "2026-07-08T10:55:32.388213", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3faaafa..31133c5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -417,8 +417,8 @@ "sex: female", "snv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", "sv_vcf: /oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "bam_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", - "bai_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai", + "bam_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam", + "bai_tumor: /oncoanalyser/results/subject_a/alignments/dna/subject_a.tumor.redux.bam.bai", "bam_normal: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam", "bai_normal: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai" ] From 934605653f959bce17a4fd841451fed4955c5397 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Thu, 9 Jul 2026 11:29:12 +0200 Subject: [PATCH 098/102] fix: `NFCORE_ONCOANALYSER` to run forked patched version of `oncoanalyser` (#8) Due to bug https://github.com/nf-core/oncoanalyser/issues/301, purple output `tbi` are not produced by `oncoanalyser` when run in stub. These files are expected by `oncorefiner` which would lead the tests to fail. I have created a forked version https://github.com/Clinical-Genomics/oncoanalyser with branch `2.2.0-with-purple-tbi-fix` that includes a fix for this bug. Version `2.2.0` was the one used for test runs on hasta, so this PR also changes the version used to match this. When `nf-core/oncoanalyser` is patched, we can revert these changes to run the updated official release of the pipeline - see https://github.com/Clinical-Genomics/MTP-oncoflow/issues/102. ### Changed - `NFCORE_ONCOANALYSER` to run forked fixed version `Clinical-Genomics/oncoanalyser `. - test config to run the above with revision `2.2.0-with-purple-tbi-fix`. --- CHANGELOG.md | 2 + conf/test.config | 2 +- tests/default.nf.test.snap | 80 +++++++++++++++++++++----------------- workflows/oncoflow.nf | 2 +- 4 files changed, 48 insertions(+), 38 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 39a77d9..1cb7e03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,8 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. +- [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed `NFCORE_ONCOANALYSER` to run forked fixed `Clinical-Genomics/oncoanalyser` instead, due to bug https://github.com/nf-core/oncoanalyser/issues/301. +- [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed test config to run the above with revision `2.2.0-with-purple-tbi-fix` which includes the fix for https://github.com/nf-core/oncoanalyser/issues/301 and `nf-core/oncoanalyser` version 2.2.0 since this was the version used for previous test runs. ### `Fixed` diff --git a/conf/test.config b/conf/test.config index d3d3b3b..9796624 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,5 +30,5 @@ params { sex = 'female' // Oncoanalyser input parameters - oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.3.0' + oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.2.0-with-purple-tbi-fix' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 31133c5..88864df 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -23,29 +23,29 @@ "oncoanalyser/results/subject_a/amber", "oncoanalyser/results/subject_a/amber/placeholder", "oncoanalyser/results/subject_a/bamtools", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv", - "oncoanalyser/results/subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.summary.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.coverage.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.flag_counts.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.frag_length.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.partition_stats.tsv", + "oncoanalyser/results/subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.summary.tsv", "oncoanalyser/results/subject_a/chord", "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv", "oncoanalyser/results/subject_a/chord/subject_a.tumor.chord.prediction.tsv", "oncoanalyser/results/subject_a/cider", - "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.blastn_match.tsv.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.layout.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.locus_stats.tsv", "oncoanalyser/results/subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz", - "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.bam", + "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.blastn_match.tsv.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.layout.gz", "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv", "oncoanalyser/results/subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz", @@ -274,28 +274,15 @@ "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.germline.tsv", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.driver.catalog.somatic.tsv", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.germline.vcf.gz.tbi", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.purity.tsv", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.qc", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz.tbi", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz.tbi", "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz", - "oncoanalyser/results/subject_a/sage", - "oncoanalyser/results/subject_a/sage/germline", - "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.gene.coverage.tsv", - "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.png", - "oncoanalyser/results/subject_a/sage/germline/subject_a.normal.sage.bqr.tsv", - "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.png", - "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv", - "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz", - "oncoanalyser/results/subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi", - "oncoanalyser/results/subject_a/sage/somatic", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.png", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.gene.coverage.tsv", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.png", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz", - "oncoanalyser/results/subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi", + "oncoanalyser/results/subject_a/purple/subject_a.tumor.purple.sv.vcf.gz.tbi", "oncoanalyser/results/subject_a/sage_append", "oncoanalyser/results/subject_a/sage_append/germline", "oncoanalyser/results/subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz", @@ -307,6 +294,23 @@ "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz", "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi", "oncoanalyser/results/subject_a/sage_append/somatic/subject_a.tumor_query.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_calling", + "oncoanalyser/results/subject_a/sage_calling/germline", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.normal.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz", + "oncoanalyser/results/subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz.tbi", + "oncoanalyser/results/subject_a/sage_calling/somatic", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.png", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.tumor.gene.coverage.tsv", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.png", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.tsv", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz", + "oncoanalyser/results/subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi", "oncoanalyser/results/subject_a/sigs", "oncoanalyser/results/subject_a/sigs/placeholder", "oncoanalyser/results/subject_a/teal", @@ -381,8 +385,16 @@ "subject_a.tumor.purple.cnv.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.driver.catalog.germline.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.driver.catalog.somatic.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.purity.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.purple.qc:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.sv.germline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.purple.sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.gene.coverage.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -395,10 +407,6 @@ "subject_a.tumor.sage.bqr.png:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.sage.somatic.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.normal.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.normal_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.tumor.sage.append.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.tumor_query.sage.bqr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "placeholder:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.teal.telbam.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.normal.teal.telbam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -423,7 +431,7 @@ "bai_normal: /oncoanalyser/results/subject_a/alignments/dna/subject_a.normal.redux.bam.bai" ] ], - "timestamp": "2026-07-07T15:56:59.927545", + "timestamp": "2026-07-08T11:12:38.15633", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 661464b..3f34117 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -32,7 +32,7 @@ workflow ONCOFLOW { def ch_versions = channel.empty() NFCORE_ONCOANALYSER( - 'nf-core/oncoanalyser', + 'Clinical-Genomics/oncoanalyser', val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, From 8e30a7e9db236f83d961461b2bc5c13b15fb2b51 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Thu, 9 Jul 2026 15:29:42 +0200 Subject: [PATCH 099/102] feat: Add `oncorefiner` (#4) ### Added - `NFCORE_ONCOREFINER` module using `NEXTFLOW_RUN` to `ONCOFLOW` workflow. - Input parameters for running `oncorefiner`: - `oncorefiner_config` - `oncorefiner_nextflow_opts` ### Changed - Updated `.nftignore` to ignore `vep` output files from `oncorefiner` - see https://github.com/Clinical-Genomics/oncorefiner/blob/f3b47fd369738465684ebaf62f04c44989d0cde6/tests/.nftignore#L12. --- CHANGELOG.md | 4 ++- conf/test.config | 3 ++ docs/parameters.md | 11 ++++++- main.nf | 14 +++++++-- nextflow.config | 4 +++ nextflow_schema.json | 27 ++++++++++++++++- tests/.nftignore | 1 + tests/default.nf.test.snap | 59 +++++++++++++++++++++++++++++++++++++- workflows/oncoflow.nf | 23 +++++++++++---- 9 files changed, 135 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1cb7e03..be4206a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,11 +15,13 @@ Initial release of Clinical-Genomics/oncoflow, created with the [nf-core](https: - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` local module. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added metadata parameters `case_id`, `sample_id_tumor`, `sample_id_normal`, `subject_id` and `sex`, necessary for creating the `oncoanalyser` params file using the `CREATE_ONCOREFINER_PARAMS_FILE` local module. - [#5](https://github.com/Clinical-Genomics/oncoflow/pull/5) Added `CREATE_ONCOREFINER_PARAMS_FILE` module to `ONCOFLOW` workflow. +- [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Added `CLINICAL_GENOMICS_ONCOREFINER` using the `NEXTFLOW_RUN` local module to run the `Clinical-Genomics/oncorefiner` pipeline in `ONCOFLOW` workflow. +- [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Added input parameters for running `Clinical-Genomics/oncorefiner`: `oncorefiner_config` and `oncorefiner_nextflow_opts`. ### `Changed` - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Changed default test to not capture `pipeline_info` files for all pipelines. -- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `pipeline_info` and `multiqc` files for all pipelines. +- [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) and [#4](https://github.com/Clinical-Genomics/oncoflow/pull/4) Updated `.nftignore` to ignore `pipeline_info`, `multiqc` and `vep` files for all pipelines. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore gzipped output files from `oncoanalyser` due to https://github.com/nf-core/oncoanalyser/issues/299. - [#3](https://github.com/Clinical-Genomics/oncoflow/pull/3) Updated `.nftignore` to ignore `*.command.*` output files from `oncoanalyser` since several files include the run directory and platform information which changes for each run and therefore cannot be snapshot. - [#8](https://github.com/Clinical-Genomics/oncoflow/pull/8) Changed `NFCORE_ONCOANALYSER` to run forked fixed `Clinical-Genomics/oncoanalyser` instead, due to bug https://github.com/nf-core/oncoanalyser/issues/301. diff --git a/conf/test.config b/conf/test.config index 9796624..7d1582e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,4 +31,7 @@ params { // Oncoanalyser input parameters oncoanalyser_nextflow_opts = '-profile test_stub,docker -stub -revision 2.2.0-with-purple-tbi-fix' + + // Oncorefiner input parameters + oncorefiner_nextflow_opts = '-profile test,docker -revision dev -stub' } diff --git a/docs/parameters.md b/docs/parameters.md index 671567f..de1d5b6 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -16,7 +16,7 @@ Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, writte ## Oncoanalyser -Necessary input files and nextflow options for running nf-core/oncoanlyser. +Input files and nextflow options for running nf-core/oncoanlyser. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| @@ -25,6 +25,15 @@ Necessary input files and nextflow options for running nf-core/oncoanlyser. | `oncoanalyser_params_file` | Path to params file for nf-core/oncoanlyser. | `string` | | | | | `oncoanalyser_samplesheet` | Path to csv samplesheet file for nf-core/oncoanalyser. | `string` | | | | +## Oncorefiner + +Input files and nextflow options for running Clinical-Genomics/oncorefiner. + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `oncorefiner_config` | Path to config file for Clinical-Genomics/oncorefiner (optional). | `string` | | | | +| `oncorefiner_nextflow_opts` | Nextflow options for running Clinical-Genomics/oncorefiner. | `string` | | True | | + ## Input/output options Define where the pipeline should find input data and save output data. diff --git a/main.nf b/main.nf index c3a97ec..fe0c205 100644 --- a/main.nf +++ b/main.nf @@ -32,6 +32,8 @@ workflow CLINICALGENOMICS_ONCOFLOW { val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline + val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample val_sample_id_normal // string: [mandatory] Sample ID of the normal sample val_subject_id // string: [mandatory] Subject ID @@ -49,6 +51,8 @@ workflow CLINICALGENOMICS_ONCOFLOW { val_oncoanalyser_nextflow_opts, val_oncoanalyser_params_file, val_oncoanalyser_samplesheet, + val_oncorefiner_config, + val_oncorefiner_nextflow_opts, val_sample_id_tumor, val_sample_id_normal, val_subject_id, @@ -57,9 +61,9 @@ workflow CLINICALGENOMICS_ONCOFLOW { ) emit: - oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(oncoanalyser_output_directory)] + oncoanalyser_output = ONCOFLOW.out.oncoanalyser_output // channel: [path(analysis_output_directory)] + oncorefiner_output = ONCOFLOW.out.oncorefiner_output // channel: [path(analysis_output_directory)] oncorefiner_params_file = ONCOFLOW.out.oncorefiner_params_file // channel: [path(yaml)] - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -93,6 +97,8 @@ workflow { params.oncoanalyser_nextflow_opts, params.oncoanalyser_params_file, params.oncoanalyser_samplesheet, + params.oncorefiner_config, + params.oncorefiner_nextflow_opts, params.sample_id_tumor, params.sample_id_normal, params.subject_id, @@ -113,6 +119,7 @@ workflow { publish: oncoanalyser_output = CLINICALGENOMICS_ONCOFLOW.out.oncoanalyser_output + oncorefiner_output = CLINICALGENOMICS_ONCOFLOW.out.oncorefiner_output oncorefiner_params_file = CLINICALGENOMICS_ONCOFLOW.out.oncorefiner_params_file } @@ -120,6 +127,9 @@ output { oncoanalyser_output { path "oncoanalyser" } + oncorefiner_output { + path "oncorefiner" + } oncorefiner_params_file { path "oncorefiner" } diff --git a/nextflow.config b/nextflow.config index c742ad5..0c20ce5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,6 +22,10 @@ params { oncoanalyser_params_file = '' oncoanalyser_samplesheet = '' + // Oncorefiner parameters + oncorefiner_config = '' + oncorefiner_nextflow_opts = '' + // Boilerplate options outdir = null publish_dir_mode = 'copy' diff --git a/nextflow_schema.json b/nextflow_schema.json index 8e64131..cf20149 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -39,7 +39,7 @@ "oncoanalyser": { "title": "Oncoanalyser", "type": "object", - "description": "Necessary input files and nextflow options for running nf-core/oncoanlyser.", + "description": "Input files and nextflow options for running nf-core/oncoanlyser.", "default": "", "properties": { "oncoanalyser_config": { @@ -75,6 +75,28 @@ "required": ["oncoanalyser_nextflow_opts"], "fa_icon": "fas fa-file-import" }, + "oncorefiner": { + "title": "Oncorefiner", + "type": "object", + "description": "Input files and nextflow options for running Clinical-Genomics/oncorefiner.", + "default": "", + "properties": { + "oncorefiner_config": { + "type": "string", + "description": "Path to config file for Clinical-Genomics/oncorefiner (optional).", + "format": "file-path", + "exists": true, + "fa_icon": "far fa-file" + }, + "oncorefiner_nextflow_opts": { + "type": "string", + "description": "Nextflow options for running Clinical-Genomics/oncorefiner.", + "fa_icon": "fas fa-terminal" + } + }, + "required": ["oncorefiner_nextflow_opts"], + "fa_icon": "fas fa-file-import" + }, "input_output_options": { "title": "Input/output options", "type": "object", @@ -229,6 +251,9 @@ { "$ref": "#/$defs/oncoanalyser" }, + { + "$ref": "#/$defs/oncorefiner" + }, { "$ref": "#/$defs/input_output_options" }, diff --git a/tests/.nftignore b/tests/.nftignore index 10d08cd..cab8d7a 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -3,3 +3,4 @@ **/multiqc/** oncoanalyser/**/*.gz oncoanalyser/**/*.command.* +oncorefiner/**/vep/*.{html} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 88864df..33fdd69 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -328,6 +328,42 @@ "oncoanalyser/results/subject_a/virusinterpreter/subject_a.tumor.virus.annotated.tsv", "oncorefiner", "oncorefiner/oncorefiner_params.yaml", + "oncorefiner/results", + "oncorefiner/results/alignments", + "oncorefiner/results/alignments/subject_a_normal.cram", + "oncorefiner/results/alignments/subject_a_normal.cram.crai", + "oncorefiner/results/alignments/subject_a_tumor.cram", + "oncorefiner/results/alignments/subject_a_tumor.cram.crai", + "oncorefiner/results/multiqc", + "oncorefiner/results/multiqc/multiqc_data", + "oncorefiner/results/multiqc/multiqc_data/.stub", + "oncorefiner/results/multiqc/multiqc_plots", + "oncorefiner/results/multiqc/multiqc_plots/.stub", + "oncorefiner/results/multiqc/multiqc_report.html", + "oncorefiner/results/pipeline_info", + "oncorefiner/results/pipeline_info/oncorefiner_software_mqc_versions.yml", + "oncorefiner/results/process_svs", + "oncorefiner/results/process_svs/test_case_id_clinical.vcf.gz", + "oncorefiner/results/process_svs/test_case_id_clinical.vcf.gz.tbi", + "oncorefiner/results/process_svs/test_case_id_research.vcf.gz", + "oncorefiner/results/process_svs/test_case_id_research.vcf.gz.tbi", + "oncorefiner/results/snv", + "oncorefiner/results/snv/test_case_id_clinical.vcf.gz", + "oncorefiner/results/snv/test_case_id_clinical.vcf.gz.tbi", + "oncorefiner/results/snv/test_case_id_genmod_score.vcf.gz", + "oncorefiner/results/snv/test_case_id_genmod_score.vcf.gz.tbi", + "oncorefiner/results/snv/test_case_id_vcfanno.vcf.gz", + "oncorefiner/results/snv/test_case_id_vcfanno.vcf.gz.tbi", + "oncorefiner/results/snv/test_case_id_vep.vcf.gz", + "oncorefiner/results/snv/test_case_id_vep.vcf.gz.tbi", + "oncorefiner/results/snv/test_case_id_vep_summary.html", + "oncorefiner/results/vcf2cytosure", + "oncorefiner/results/vcf2cytosure/normal.cgh", + "oncorefiner/results/vcf2cytosure/tumor.cgh", + "oncorefiner/results/vep", + "oncorefiner/results/vep/test_case_id_svdbquery_vep.vcf.gz", + "oncorefiner/results/vep/test_case_id_svdbquery_vep.vcf.gz.tbi", + "oncorefiner/results/vep/test_case_id_svdbquery_vep_summary.html", "pipeline_info", "pipeline_info/oncoflow_software_versions.yml" ], @@ -416,7 +452,28 @@ "subject_a.tumor.teal.tellength.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", "subject_a.tumor.virusbreakend.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", - "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "subject_a.tumor.virus.annotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_normal.cram:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_normal.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_tumor.cram:md5,d41d8cd98f00b204e9800998ecf8427e", + "subject_a_tumor.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_clinical.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_clinical.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_research.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_research.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_clinical.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_clinical.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_genmod_score.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_genmod_score.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_vcfanno.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_vcfanno.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "normal.cgh:md5,d41d8cd98f00b204e9800998ecf8427e", + "tumor.cgh:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_case_id_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_case_id_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ "case_id: test_case_id", diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 3f34117..6888b8b 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -3,9 +3,10 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" -include { CREATE_ONCOREFINER_PARAMS_FILE } from "../modules/local/createoncorefinerparamsfile/main" -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { CREATE_ONCOREFINER_PARAMS_FILE } from "../modules/local/createoncorefinerparamsfile/main" +include { NEXTFLOW_RUN as CLINICAL_GENOMICS_ONCOREFINER } from '../modules/local/nextflow/run' +include { NEXTFLOW_RUN as NFCORE_ONCOANALYSER } from "../modules/local/nextflow/run/main" +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21,6 +22,8 @@ workflow ONCOFLOW { val_oncoanalyser_nextflow_opts // string: [mandatory] Nextflow options for oncoanalyser pipeline val_oncoanalyser_params_file // string: [mandatory] Parameters file for oncoanalyser pipeline val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline + val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline + val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample val_sample_id_normal // string: [mandatory] Sample ID of the normal sample val_subject_id // string: [mandatory] Subject ID @@ -50,6 +53,15 @@ workflow ONCOFLOW { outdir ) + CLINICAL_GENOMICS_ONCOREFINER( + 'Clinical-Genomics/oncorefiner', + val_oncorefiner_nextflow_opts, + CREATE_ONCOREFINER_PARAMS_FILE.out.params_file, + '', + val_oncorefiner_config, + workflow.workDir.resolve('Clinical-Genomics/oncorefiner').toUriString(), + ) + // // Collate and save software versions // @@ -80,9 +92,10 @@ workflow ONCOFLOW { ) emit: - oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(oncoanalyser_output_directory)] + oncoanalyser_output = NFCORE_ONCOANALYSER.out.output // channel: [path(analysis_output_directory)] + oncorefiner_output = CLINICAL_GENOMICS_ONCOREFINER.out.output // channel: [path(analysis_output_directory)] oncorefiner_params_file = CREATE_ONCOREFINER_PARAMS_FILE.out.params_file // channel: [path(yaml)] - versions = ch_versions + versions = ch_versions // channel: [path(versions.yml)] } /* From 64a6f65cbc9b95e8c2524704ba87982e50f813a3 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 9 Jul 2026 16:40:09 +0200 Subject: [PATCH 100/102] Change to val_outdir. --- main.nf | 4 ++-- workflows/oncoflow.nf | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index fe0c205..e958f6e 100644 --- a/main.nf +++ b/main.nf @@ -34,11 +34,11 @@ workflow CLINICALGENOMICS_ONCOFLOW { val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline + val_outdir // string: [mandatory] The output directory where the results will be saved val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample val_sample_id_normal // string: [mandatory] Sample ID of the normal sample val_subject_id // string: [mandatory] Subject ID val_sex // string: [mandatory] Sex of the patient - outdir // string: [mandatory] The output directory where the results will be saved main: @@ -57,7 +57,7 @@ workflow CLINICALGENOMICS_ONCOFLOW { val_sample_id_normal, val_subject_id, val_sex, - outdir + val_outdir ) emit: diff --git a/workflows/oncoflow.nf b/workflows/oncoflow.nf index 6888b8b..ac85ba0 100644 --- a/workflows/oncoflow.nf +++ b/workflows/oncoflow.nf @@ -24,11 +24,11 @@ workflow ONCOFLOW { val_oncoanalyser_samplesheet // string: [mandatory] Samplesheet file for oncoanalyser pipeline val_oncorefiner_config // string: [optional] Config file for oncorefiner pipeline val_oncorefiner_nextflow_opts // string: [mandatory] Nextflow options for oncorefiner pipeline + val_outdir // string: [mandatory] The output directory where the results will be saved val_sample_id_tumor // string: [mandatory] Sample ID of the tumor sample val_sample_id_normal // string: [mandatory] Sample ID of the normal sample val_subject_id // string: [mandatory] Subject ID val_sex // string: [mandatory] Sex of the patient - outdir // string: [mandatory] The output directory where the results will be saved main: @@ -50,7 +50,7 @@ workflow ONCOFLOW { val_sample_id_normal, val_sex, NFCORE_ONCOANALYSER.out.output, - outdir + val_outdir ) CLINICAL_GENOMICS_ONCOREFINER( @@ -85,7 +85,7 @@ workflow ONCOFLOW { def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${outdir}/pipeline_info", + storeDir: "${val_outdir}/pipeline_info", name: 'oncoflow_software_' + 'versions.yml', sort: true, newLine: true From 04996035e154d45e01d29b7c1bb8f2a41636fb64 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 9 Jul 2026 16:52:55 +0200 Subject: [PATCH 101/102] Add assets/test_oncoflow_params.yaml. --- assets/test_oncoflow_params.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 assets/test_oncoflow_params.yaml diff --git a/assets/test_oncoflow_params.yaml b/assets/test_oncoflow_params.yaml new file mode 100644 index 0000000..714e076 --- /dev/null +++ b/assets/test_oncoflow_params.yaml @@ -0,0 +1,8 @@ +case_id: "test_case_id" +sample_id_tumor: "test_sample_id_tumor" +sample_id_normal: "test_sample_id_normal" +sex: "female" + +oncoanalyser_create_stub_placeholders: true +oncoanalyser_genome: "GRCh38_hmf" +oncoanalyser_mode: "wgts" From 066fda67eb523a4490680a57b12c554c2420d711 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 9 Jul 2026 17:03:08 +0200 Subject: [PATCH 102/102] Add draft assets/test_oncoflow.config --- assets/test_oncoflow.config | 93 +++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 assets/test_oncoflow.config diff --git a/assets/test_oncoflow.config b/assets/test_oncoflow.config new file mode 100644 index 0000000..32aa5e4 --- /dev/null +++ b/assets/test_oncoflow.config @@ -0,0 +1,93 @@ +// +// Oncoanalyser configuration +// + +// TODO + +// +// Oncorefiner configuration +// + +// TODO +params { + // Parameters and options for tools + extra_args_cadd_annotate = '--columns Chrom,Pos,Ref,Alt,-,CADD' + extra_args_snv_clinical_filter = "--include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")'" + extra_args_snv_research_filter = "--include '(INFO/GNOMADAF_grpmax <= 0.001 || INFO/GNOMADAF_grpmax == \".\")'" + extra_args_snv_vep = '' + extra_args_sv_vep = '' + + // Pipeline resource files + // VEP + vep_cache_version = 115 + vep_plugin_files = params.oncoflow_resources_dir + 'vep_plugin.csv' + vep_cache = params.oncoflow_resources_dir + 'VEP' + + // Vcfanno + vcfanno_toml = params.oncoflow_resources_dir + 'grch38_vcfanno_config.toml' + vcfanno_resources = params.oncoflow_resources_dir + 'grch38_vcfanno_resources.txt' + vcfanno_lua = null + + // SVDB + svdb_query_dbs = params.oncoflow_resources_dir + 'grch38_svdb_query_dbs.csv' + + // Reference + fasta = params.oncoflow_resources_dir + 'GRCh38_masked_exclusions_alts_hlas.fasta' + fai = params.oncoflow_resources_dir + 'GRCh38_masked_exclusions_alts_hlas.fasta.fai' +} + + +process { + + withName: '.*:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' { + errorStrategy = 'ignore' + } + + withName:'.*PROCESS_SNVS:BCFTOOLS_VIEW_RESEARCH' { + ext.args = { [ + "${params.extra_args_snv_research_filter}", + "--output-type z", + "--write-index=tbi", + ].join(' ') } + } + + withName: '.*PROCESS_SNVS:ENSEMBLVEP_VEP' { + maxForks = 8 + memory = { 10.GB * task.attempt } + cpus = { 2 * task.attempt } + time = { 4.h * task.attempt } + } + + + withName: '.*PROCESS_SVS:ENSEMBLVEP_VEP' { + maxForks = 8 + memory = { 10.GB * task.attempt } + cpus = { 2 * task.attempt } + time = { 4.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:CADD' { + memory = { 30.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:RENAME_CHR_CADD' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:ANNOTATE_INDELS' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + + withName: '.*ANNOTATE_CADD:BCFTOOLS_VIEW' { + memory = { 1.GB * task.attempt } + cpus = { 1 * task.attempt } + time = { 1.h * task.attempt } + } + +}