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more docs for somatic exome #872

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more docs for somatic exome #872

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more docs for somatic exome
zlskidmore Feb 4, 2020
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Update definitions/pipelines/somatic_exome.cwl
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Merge branch 'somatic_exome_doc' of github.com:genome/analysis-workfl…
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23 changes: 22 additions & 1 deletion definitions/pipelines/somatic_exome.cwl
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Expand Up @@ -92,7 +92,7 @@ inputs:
secondaryFiles: [.tbi]
label: "dbsnp_vcf: File specifying common polymorphic indels from dbSNP"
doc: |
dbsnp_vcf provides known indels reecommended by GATK for a variety of tools
dbsnp_vcf provides known indels recommended by GATK for a variety of tools
including the BaseRecalibrator. This file is part of the GATK resource bundle
available at http://www.broadinstitute.org/gatk/guide/article?id=1213
Essintially it is a list of known indels from dbSNP. File should be in vcf format,
Expand Down Expand Up @@ -124,21 +124,42 @@ inputs:
In general for a WES exome reagent bait_intervals and target_intervals are the same.
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
label: "per_base_intervals: yaml file specifying name and input for picard CollectHsMetrics"
doc: |
Optional input, redundant with bait_intervals, provides a way to name name the output file from running picard CollectHsMetrics. Also triggers picard to output per-base metrics. See ../types/labelled_file.yml for an example.
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
label: "per_target_intervals: yaml file specifying name and input for picard CollectHsMetrics"
doc: |
Optional input, redundant with target_intervals, provides a way to name name the output file from running picard CollectHsMetrics. Also triggers picard to output per-base metrics. See ../types/labelled_file.yml for an example.
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
label: "summary_intervals: yaml file specifying name and input for picard CollectHsMetrics"
doc: |
Optional input, redundant with bait_intervals and target_intervals, supplies the same file for BAIT_INTERVALS= and TARGET_INTERVALS= parameters in picard CollectHsMetrics. Provides a way to name name the output file from running the picard command. See ../types/labelled_file.yml for an example.
omni_vcf:
type: File
secondaryFiles: [.tbi]
label: "omni_vcf: An omni VCF file from 1000 genomes specifying genotype information"
doc: |
A vcf file from the illumina omni platform specifying genotype information. Used for the identification of sample swaps with the the tool verifyBamId. VCf files suitable for this can be found here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/. File must be tabix indexed and on the same genome assembly as the alignments you are producing.
picard_metric_accumulation_level:
type: string
label: "picard_metric_accumulation_level: picard tool flag specifying how to aggregate QC metrics"
doc: |
A string, one of ALL_READS, SAMPLE, LIBRARY, READ_GROUP, specifying how relevant picard tools should summarize QC metrics. Currently used in picards CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics
qc_minimum_mapping_quality:
type: int?
default: 0
label: "qc_minimum_mapping_quality: minimum read mapping quality picard uses when summarizing QC metrics"
doc: |
An integer specifying the minimum read mapping quality picard requires to summarize QC metrics. Commonly set at 20.
qc_minimum_base_quality:
type: int?
default: 0
label: "qc_minimum_base_quality: minimum base quality picard uses when summarizing QC metrics"
doc: |
An integer specifying the minimum base quality within a read picard requires to summarize QC metrics. Commonly set at 20.
interval_list:
type: File
cosmic_vcf:
Expand Down