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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
fastqc_reports:
type: { type: array, items: { type: array, items: File } }
trim_reports:
type: { type: array, items: { type: array, items: File } }
hs_metrics: File[]
bams_markduplicates: File[]
raw_variants: File[]
bams_recalibrated: File[]
outputs:
fastqc_reports_dir:
type: Directory
outputSource: org_fastqc_reports/outdir
trim_reports_dir:
type: Directory
outputSource: org_trim_reports/outdir
hs_metrics_dir:
type: Directory
outputSource: org_hs_metrics/outdir
bams_markduplicates_dir:
type: Directory
outputSource: org_bams_markduplicates/outdir
raw_variants_dir:
type: Directory
outputSource: org_raw_variants/outdir
bams_recalibrated_dir:
type: Directory
outputSource: org_bams_recalibrated/outdir
steps:
org_fastqc_reports:
run: ../tools/file-pairs-to-directory.cwl
in:
name:
default: 'fastqc-reports'
file_pairs: fastqc_reports
out:
- outdir
org_trim_reports:
run: ../tools/file-pairs-to-directory.cwl
in:
name:
default: 'trim-reports'
file_pairs: trim_reports
out:
- outdir
org_hs_metrics:
run: ../tools/files-to-directory.cwl
in:
name:
default: 'hs-metrics'
files: hs_metrics
out:
- outdir
org_bams_markduplicates:
run: ../tools/files-to-directory.cwl
in:
name:
default: 'bams-markduplicates'
files: bams_markduplicates
out:
- outdir
org_raw_variants:
run: ../tools/files-to-directory.cwl
in:
name:
default: 'gvcfs'
files: raw_variants
out:
- outdir
org_bams_recalibrated:
run: ../tools/files-to-directory.cwl
in:
name:
default: 'bams-recalibrated'
files: bams_recalibrated
out:
- outdir
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