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bam_readcount.cwl
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bam_readcount.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "bam_readcount workflow"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
vcf:
type: File
secondaryFiles: [.tbi]
sample:
type: string
reference_fasta:
type: string
bam:
type: File
secondaryFiles: [.bai]
min_base_quality:
type: int?
min_mapping_quality:
type: int?
outputs:
normalized_vcf:
type: File
outputSource: decompose_variants/decomposed_vcf
snv_bam_readcount_tsv:
type: File
outputSource: bam_readcount/snv_bam_readcount_tsv
indel_bam_readcount_tsv:
type: File
outputSource: bam_readcount/indel_bam_readcount_tsv
steps:
normalize_variants:
run: ../tools/normalize_variants.cwl
in:
reference: reference_fasta
vcf: vcf
out:
[normalized_vcf]
decompose_variants:
run: ../tools/vt_decompose.cwl
in:
vcf: normalize_variants/normalized_vcf
out:
[decomposed_vcf]
bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: decompose_variants/decomposed_vcf
sample: sample
reference_fasta: reference_fasta
bam: bam
min_base_quality: min_base_quality
min_mapping_quality: min_mapping_quality
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]