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Customizable post-processing and extension layer for Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core.
Input/output options
Define where the pipeline should find input data and save output data.
Parameter
Description
Type
Default
Required
Hidden
outdir
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
True
email
Email address for completion summary. HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
string
multiqc_title
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Metadata
Parameter
Description
Type
Default
Required
Hidden
case_id
Case ID.
string
True
sex
Sex of the patient. (accepted: female|male|unknown)
string
True
sample_id_tumor
Sample id of the tumor sample.
string
True
sample_id_normal
Sample id of the normal sample.
string
Input files
Parameter
Description
Type
Default
Required
Hidden
snv_vcf
Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.
string
sv_vcf
Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.
string
bam_tumor
Path to alignment BAM file for the tumor sample.
string
bai_tumor
Path to BAM index file for the tumor sample.
string
bam_normal
Path to alignment BAM file for the normal sample.
string
bai_normal
Path to BAM index file for the normal sample.
string
Reference genome options
Reference genome related files and options required for the workflow.
Parameter
Description
Type
Default
Required
Hidden
genome
Name of the genome reference. (accepted: GRCh38|GRCh37) HelpUse this parameter to specify the ID for the reference genome used. This is then used to annotate the SV and SNV files e.g. --genome GRCh38.
string
GRCh38
genome_version_number
Genome version number. By default parsed from params.genome by removing "GRCh" from genome name to obtain only the version number (e.g. "GRCh38" -> "38"). (accepted: 37|38)
integer
38
True
fasta
Path to FASTA genome file. HelpIf you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
string
fai
Path to FASTA genome index file. HelpIf none provided, will be generated automatically from the FASTA reference
Species of the reference genome. E.g. --species homo_sapiens. (accepted: homo_sapiens)
string
homo_sapiens
Annotation options
Annotation related files and options required for the workflow.
Parameter
Description
Type
Default
Required
Hidden
vep_cache_version
Specify the version of the VEP cache provided to the --vep_cache option.
integer
112
vep_cache
Path to vep's cache directory. HelpIf no directory path is passed, vcf files will not be annotated by vep.
string
vep_plugin_files
Databases used by both named and custom plugins to annotate variants. HelpPath to a CSV/TSV/JSON/YAML file with vep_files as header, and then the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file.
string
vcfanno_extra
Path to a VCF file containing annotations. HelpCan be used to supply case-specific annotations in addition to those provided using --vcfanno_resources
string
vcfanno_resources
Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource. HelpIf no file is passed, default configurations will be used according to genome build within the context of the pipeline.
string
vcfanno_toml
Path to the vcfanno toml file. HelpIf no toml is passed, default configurations will be used according to genome build within the context of the pipeline.
string
vcfanno_lua
Path to the vcfanno lua file. HelpCustom operations file (lua). For use when the built-in ops don't supply the needed reduction.
string
svdb_query_dbs
Databases used for structural variant annotation in vcf format. HelpPath to CSV, TSV, JSON or YAML file containing information about the databases used for structural variant annotation.
string
extra_args_cadd_annotate
Extra arguments for ANNOTATE_CADD:BCFTOOLS_ANNOTATE_INDELS.
string
extra_args_snv_clinical_filter
Extra arguments for PROCESS_SNVS:BCFTOOLS_VIEW_CLINICAL.
string
extra_args_snv_research_filter
Extra arguments for PROCESS_SNVS:BCFTOOLS_VIEW_RESEARCH.
string
extra_args_snv_vep
Extra arguments for PROCESS_SNVS:ENSEMBLVEP_VEP.
string
extra_args_sv_vep
Extra arguments for PROCESS_SVS:ENSEMBLVEP_VEP.
string
genmod_score_config
Path to genmod score configuration file (rank model).
string
Institutional config options
Parameters used to describe centralised config profiles. These should not be edited.
Parameter
Description
Type
Default
Required
Hidden
custom_config_version
Git commit id for Institutional configs.
string
master
True
custom_config_base
Base directory for Institutional configs. HelpIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Less common options for the pipeline, typically set in a config file.
Parameter
Description
Type
Default
Required
Hidden
version
Display version and exit.
boolean
True
publish_dir_mode
Method used to save pipeline results to output directory. (accepted: symlink|rellink|link|copy|copyNoFollow|move) HelpThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
string
copy
True
email_on_fail
Email address for completion summary, only when pipeline fails. HelpAn email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
string
True
plaintext_email
Send plain-text email instead of HTML.
boolean
True
max_multiqc_email_size
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
True
monochrome_logs
Do not use coloured log outputs.
boolean
True
multiqc_config
Custom config file to supply to MultiQC.
string
True
multiqc_logo
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
True
multiqc_methods_description
Custom MultiQC yaml file containing HTML including a methods description.
string
validate_params
Boolean whether to validate parameters against the schema at runtime
boolean
True
True
pipelines_testdata_base_path
Base URL or local path to location of pipeline test dataset files