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bam_to_bqsr.cwl
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bam_to_bqsr.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Unaligned BAM to BQSR"
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
bams:
type: File[]
readgroups:
type: string[]
bqsr_intervals:
type: string[]?
reference:
type: string
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
final_name:
type: string
default: 'final.bam'
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
outputs:
final_bam:
type: File
outputSource: index_bam/indexed_bam
secondaryFiles: [.bai, ^.bai]
mark_duplicates_metrics_file:
type: File
outputSource: mark_duplicates_and_sort/metrics_file
steps:
align:
scatter: [bam, readgroup]
scatterMethod: dotproduct
run: align.cwl
in:
bam: bams
readgroup: readgroups
reference: reference
out:
[tagged_bam]
merge:
run: ../tools/merge_bams_samtools.cwl
in:
bams: align/tagged_bam
name: final_name
out:
[merged_bam]
name_sort:
run: ../tools/name_sort.cwl
in:
bam: merge/merged_bam
out:
[name_sorted_bam]
mark_duplicates_and_sort:
run: ../tools/mark_duplicates_and_sort.cwl
in:
bam: name_sort/name_sorted_bam
out:
[sorted_bam, metrics_file]
bqsr:
run: ../tools/bqsr.cwl
in:
reference: reference
bam: mark_duplicates_and_sort/sorted_bam
intervals: bqsr_intervals
known_sites: [dbsnp_vcf, mills, known_indels]
out:
[bqsr_table]
apply_bqsr:
run: ../tools/apply_bqsr.cwl
in:
reference: reference
bam: mark_duplicates_and_sort/sorted_bam
bqsr_table: bqsr/bqsr_table
output_name: final_name
out:
[bqsr_bam]
index_bam:
run: ../tools/index_bam.cwl
in:
bam: apply_bqsr/bqsr_bam
out:
[indexed_bam]