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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment with qc"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: File
secondaryFiles: [.fai, .bwt, .sa, .ann, .amb, .pac, ^.dict, .alt]
bams:
type: File[]
readgroups:
type: string[]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp:
type: File
secondaryFiles: [.tbi]
bait_intervals:
type: File
target_intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
outputs:
bam:
type: File
outputSource: alignment/final_bam
insert_size_metrics:
type: File
outputSource: qc/insert_size_metrics
alignment_summary_metrics:
type: File
outputSource: qc/alignment_summary_metrics
hs_metrics:
type: File
outputSource: qc/hs_metrics
per_target_coverage_metrics:
type: File
outputSource: qc/per_target_coverage_metrics
flagstats:
type: File
outputSource: qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: qc/verify_bam_id_depth
steps:
alignment:
run: unaligned_bam_to_bqsr/workflow.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
mills: mills
known_indels: known_indels
dbsnp: dbsnp
out: [final_bam]
qc:
run: qc/workflow_exome.cwl
in:
bam: alignment/final_bam
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
omni_vcf: omni_vcf
out: [insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]