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bam_to_bqsr_no_dup_marking.cwl
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bam_to_bqsr_no_dup_marking.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Unaligned BAM to BQSR and VCF"
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
bams:
type: File[]
readgroups:
type: string[]
reference:
type: string
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
outputs:
final_cram:
type: File
outputSource: index_cram/indexed_cram
secondaryFiles: [.crai, ^.crai]
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.cwl
in:
bams: align/tagged_bam
out:
[merged_bam]
position_sort:
run: ../tools/position_sort.cwl
in:
bam: merge/merged_bam
out:
[position_sorted_bam]
index_bam:
run: ../tools/index_bam.cwl
in:
bam: position_sort/position_sorted_bam
out:
[indexed_bam]
bqsr:
run: ../tools/bqsr.cwl
in:
reference: reference
bam: index_bam/indexed_bam
known_sites: [dbsnp_vcf, mills, known_indels]
out:
[bqsr_table]
apply_bqsr:
run: ../tools/apply_bqsr.cwl
in:
reference: reference
bam: index_bam/indexed_bam
bqsr_table: bqsr/bqsr_table
out:
[bqsr_bam]
bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
reference: reference
bam: apply_bqsr/bqsr_bam
out:
[cram]
index_cram:
run: ../tools/index_cram.cwl
in:
cram: bam_to_cram/cram
out:
[indexed_cram]