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exome_alignment.cwl
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exome_alignment.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment with qc"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]?
bait_intervals:
type: File
target_intervals:
type: File
per_target_intervals:
type: File
per_target_bait_intervals:
type: File
per_base_intervals:
type: File
per_base_bait_intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
outputs:
cram:
type: File
outputSource: alignment/final_cram
mark_duplicates_metrics:
type: File
outputSource: alignment/mark_duplicates_metrics_file
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
per_target_hs_metrics:
type: File?
outputSource: qc/per_target_hs_metrics
per_base_coverage_metrics:
type: File?
outputSource: qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File?
outputSource: qc/per_base_hs_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
bqsr_intervals: bqsr_intervals
out: [final_cram,mark_duplicates_metrics_file]
qc:
run: qc/workflow_exome.cwl
in:
cram: alignment/final_cram
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
per_target_intervals: per_target_intervals
per_target_bait_intervals: per_target_bait_intervals
per_base_intervals: per_base_intervals
per_base_bait_intervals: per_base_bait_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
out: [insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]