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Add category for error messages #300

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1470d83
Add category for error messages
leexgh Jun 15, 2026
7e0d708
update comments
leexgh Jun 22, 2026
f5fa4cc
Add refseq to additional_transcript column
leexgh Jul 2, 2026
905fd91
Test and model update
leexgh Aug 4, 2026
5a7cbba
Update test - hgvsp changed because Splice_Region is removed from 'sp…
leexgh Aug 4, 2026
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26 changes: 13 additions & 13 deletions .circleci/config.yml
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Expand Up @@ -47,36 +47,36 @@ jobs:
# run test
- run:
name: "check if maf file still the same when annotating with uniprot transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.uniprot.txt || (echo MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/data_mutations_extended_100.out.uniprot.txt) <(git show HEAD:test/data/data_mutations_extended_100.out.uniprot.txt | tail -n +2) || (echo MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.txt && exit 1)'

- run:
name: "check if maf file still the same when annotating with mskcc transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.mskcc.txt || (echo MAF mskcc output changed test/data/data_mutations_extended_100.out.mskcc.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/data_mutations_extended_100.out.mskcc.txt) <(git show HEAD:test/data/data_mutations_extended_100.out.mskcc.txt | tail -n +2) || (echo MAF mskcc output changed test/data/data_mutations_extended_100.out.mskcc.txt && exit 1)'

# run test
- run:
name: "check if minimal example maf file still the same when annotating with mskcc transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/minimal_example.in.txt --output-filename test/data/minimal_example.out.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/minimal_example.out.mskcc.txt || (echo simple MAF mskcc output changed test/data/minimal_example.out.mskcc.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/minimal_example.in.txt --output-filename test/data/minimal_example.out.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/minimal_example.out.mskcc.txt) <(git show HEAD:test/data/minimal_example.out.mskcc.txt | tail -n +2) || (echo simple MAF mskcc output changed test/data/minimal_example.out.mskcc.txt && exit 1)'

- run:
name: "check if columns prefixed by IGNORE_Genome_Nexus_Original are immutable"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/immutable_columns_test.in.txt --output-filename test/data/immutable_columns_test.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/immutable_columns_test.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/immutable_columns_test.out.uniprot.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/immutable_columns_test.in.txt --output-filename test/data/immutable_columns_test.out.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/immutable_columns_test.out.uniprot.txt) <(git show HEAD:test/data/immutable_columns_test.out.uniprot.txt | tail -n +2) || (echo simple MAF uniprot output changed test/data/immutable_columns_test.out.uniprot.txt && exit 1)'

- run:
name: "check if corner cases example maf file still the same when annotating with uniprot transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.two_tumor_seq_allele.in.txt --output-filename test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.two_tumor_seq_allele.in.txt --output-filename test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt) <(git show HEAD:test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt | tail -n +2) || (echo simple MAF uniprot output changed test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt && exit 1)'

- run:
name: "check if corner cases example maf file still the same when annotating with mskcc transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.two_tumor_seq_allele.in.txt --output-filename test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt || (echo simple MAF mskcc output changed test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.two_tumor_seq_allele.in.txt --output-filename test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt) <(git show HEAD:test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt | tail -n +2) || (echo simple MAF mskcc output changed test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt && exit 1)'

- run:
name: "check if corner cases example maf file still the same when annotating with uniprot transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.in.txt --output-filename test/data/corner_cases.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/corner_cases.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/corner_cases.out.uniprot.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.in.txt --output-filename test/data/corner_cases.out.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/corner_cases.out.uniprot.txt) <(git show HEAD:test/data/corner_cases.out.uniprot.txt | tail -n +2) || (echo simple MAF uniprot output changed test/data/corner_cases.out.uniprot.txt && exit 1)'

- run:
name: "check if corner cases example maf file still the same when annotating with mskcc transcripts"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.in.txt --output-filename test/data/corner_cases.out.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/corner_cases.out.mskcc.txt || (echo simple MAF mskcc output changed test/data/corner_cases.out.mskcc.txt && exit 1)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/corner_cases.in.txt --output-filename test/data/corner_cases.out.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/corner_cases.out.mskcc.txt) <(git show HEAD:test/data/corner_cases.out.mskcc.txt | tail -n +2) || (echo simple MAF mskcc output changed test/data/corner_cases.out.mskcc.txt && exit 1)'

# - run:
# name: "Run vcf2maf test cases"
Expand All @@ -85,23 +85,23 @@ jobs:
# run test
- run:
name: "check if maf file still the same when annotating with uniprot transcripts and POSTs"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.post.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.uniprot.txt || (echo MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.txt)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.post.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/data_mutations_extended_100.out.post.uniprot.txt) <(git show HEAD:test/data/data_mutations_extended_100.out.uniprot.txt | tail -n +2) || (echo MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.txt)'

- run:
name: "check if maf file still the same when annotating with mskcc transcripts and POSTs"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.post.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.mskcc.txt || (echo MAF mskcc output changed test/data/data_mutations_extended_100.out.mskcc.txt)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.post.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/data_mutations_extended_100.out.post.mskcc.txt) <(git show HEAD:test/data/data_mutations_extended_100.out.mskcc.txt | tail -n +2) || (echo MAF mskcc output changed test/data/data_mutations_extended_100.out.mskcc.txt)'

- run:
name: "check if minimal example maf file still the same when annotating with mskcc transcripts and POSTs"
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/minimal_example.in.txt --output-filename test/data/minimal_example.out.post.mskcc.txt --isoform-override mskcc && git diff -G "^[^#]" --exit-code test/data/minimal_example.out.mskcc.txt || (echo simple MAF mskcc output changed test/data/minimal_example.out.mskcc.txt)'
command: 'java -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/minimal_example.in.txt --output-filename test/data/minimal_example.out.post.mskcc.txt --isoform-override mskcc && diff <(tail -n +2 test/data/minimal_example.out.post.mskcc.txt) <(git show HEAD:test/data/minimal_example.out.mskcc.txt | tail -n +2) || (echo simple MAF mskcc output changed test/data/minimal_example.out.mskcc.txt)'

- run:
name: "check if my_variant_info provides gnomad annotations"
command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,my_variant_info -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/my_variant_info_corner_cases.in.txt --output-filename test/data/my_variant_info_corner_cases.out.uniprot.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/my_variant_info_corner_cases.out.uniprot.txt || (echo simple MAF uniprot output changed test/data/my_variant_info_corner_cases.out.uniprot.txt)'
command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,my_variant_info -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/my_variant_info_corner_cases.in.txt --output-filename test/data/my_variant_info_corner_cases.out.uniprot.txt --isoform-override uniprot && diff <(tail -n +2 test/data/my_variant_info_corner_cases.out.uniprot.txt) <(git show HEAD:test/data/my_variant_info_corner_cases.out.uniprot.txt | tail -n +2) || (echo simple MAF uniprot output changed test/data/my_variant_info_corner_cases.out.uniprot.txt)'

- run:
name: "check if nucleotide_context provides Ref_Tri and Var_Tri columnsj"
command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,nucleotide_context -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt --isoform-override uniprot && git diff -G "^[^#]" --exit-code test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt || (echo simple MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt)'
command: 'java -Dgenomenexus.enrichment_fields=annotation_summary,nucleotide_context -jar annotationPipeline/target/annotationPipeline-*.jar --filename test/data/data_mutations_extended_100.in.txt --output-filename test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt --isoform-override uniprot && diff <(tail -n +2 test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt) <(git show HEAD:test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt | tail -n +2) || (echo simple MAF uniprot output changed test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt)'

- run:
name: "performance benchmark: annotate CHOL TCGA GDC (~3764 variants) against grch38.genomenexus.org"
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -138,7 +138,7 @@ docker run -e GENOMENEXUS_BASE=https://grch38.genomenexus.org -v ${PWD}:/wd geno
|Protein_position|VEP||
|Codons|VEP||
|Exon_Number|VEP||
|Additional_Transcripts||Contains a semicolon-separated list of alternate transcripts. Each entry is a comma-separated list of: Transcript ID, Hugo Gene Symbol, HGVSp Short, HGVSc, Variant Classification. **Requires `-m extended` / `--mode extended` flag**|
|Additional_Transcripts||Contains a semicolon-separated list of alternate transcripts. Each entry is a comma-separated list of: Transcript ID, RefSeq, Hugo Gene Symbol, HGVSp Short, HGVSc, Variant Classification. **Requires `-m extended` / `--mode extended` flag**|
|gnomAD_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_AFR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
|gnomAD_AMR_AF|myvariant.info|Need to add "my_variant_info" in "genomenexus.enrichment_fields"|
Expand Down
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