/
germline_exome_gvcf.cwl
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germline_exome_gvcf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and germline variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/trimming_options.yml
- class: SubworkflowFeatureRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
bqsr_known_sites:
type: File[]
secondaryFiles: [.tbi]
doc: "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis."
bqsr_intervals:
type: string[]?
bait_intervals:
type: File
target_intervals:
type: File
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
emit_reference_confidence:
type:
type: enum
symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
ploidy:
type: int?
synonyms_file:
type: File?
qc_minimum_mapping_quality:
type: int?
qc_minimum_base_quality:
type: int?
outputs:
cram:
type: File
outputSource: index_cram/indexed_cram
mark_duplicates_metrics:
type: File
outputSource: alignment_and_qc/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: alignment_and_qc/insert_size_metrics
insert_size_histogram:
type: File
outputSource: alignment_and_qc/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: alignment_and_qc/alignment_summary_metrics
hs_metrics:
type: File
outputSource: alignment_and_qc/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: alignment_and_qc/summary_hs_metrics
flagstats:
type: File
outputSource: alignment_and_qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: alignment_and_qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: alignment_and_qc/verify_bam_id_depth
gvcf:
type: File[]
outputSource: generate_gvcfs/gvcf
steps:
alignment_and_qc:
run: alignment_exome.cwl
in:
reference: reference
sequence: sequence
trimming: trimming
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
out:
[bam, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
extract_freemix:
in:
verify_bam_id_metrics: alignment_and_qc/verify_bam_id_metrics
out:
[freemix_score]
run:
class: ExpressionTool
requirements:
- class: InlineJavascriptRequirement
inputs:
verify_bam_id_metrics:
type: File
inputBinding:
loadContents: true
outputs:
freemix_score:
type: string?
expression: |
${
var metrics = inputs.verify_bam_id_metrics.contents.split("\n");
if ( metrics[0].split("\t")[6] == 'FREEMIX' ) {
return {'freemix_score': metrics[1].split("\t")[6]};
} else {
return {'freemix_score:': null };
}
}
generate_gvcfs:
run: ../subworkflows/gatk_haplotypecaller_iterator.cwl
in:
bam: alignment_and_qc/bam
reference: reference
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: extract_freemix/freemix_score
ploidy: ploidy
out:
[gvcf]
bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: alignment_and_qc/bam
reference: reference
out:
[cram]
index_cram:
run: ../tools/index_cram.cwl
in:
cram: bam_to_cram/cram
out:
[indexed_cram]