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module-2.cwl
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module-2.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
run_tools:
type:
type: record
fields:
perl_5: string
java_7: string
java_8: string
marianas_path: string
trimgalore_path: string
bwa_path: string
arrg_path: string
picard_path: string
gatk_path: string
abra_path: string
fx_path: string
fastqc_path: string?
cutadapt_path: string?
bams:
type:
type: array
items: File
secondaryFiles:
- ^.bai
tmp_dir: string
reference_fasta: string
patient_id: string
fci__minbq: int
fci__minmq: int
fci__cov: int
fci__rf: string[]
fci__intervals: string[]?
abra__kmers: string
abra__mad: int
fix_mate_information__sort_order: string
fix_mate_information__validation_stringency: string
fix_mate_information__compression_level: int
fix_mate_information__create_index: boolean
bqsr__nct: int
bqsr__rf: string
bqsr__knownSites_dbSNP:
type: File
secondaryFiles:
- .idx
bqsr__knownSites_millis:
type: File
secondaryFiles:
- .idx
print_reads__nct: int
print_reads__EOQ: boolean
print_reads__baq: string
outputs:
standard_bams:
type: File[]
secondaryFiles:
- ^.bai
outputSource: BQSR_workflow/bqsr_bams
covint_list:
type: File
outputSource: ABRA_workflow/covint_list
covint_bed:
type: File
outputSource: ABRA_workflow/covint_bed
steps:
ABRA_workflow:
run: ABRA/abra_workflow.cwl
in:
run_tools: run_tools
bams: bams
tmp_dir: tmp_dir
reference_fasta: reference_fasta
patient_id: patient_id
fci__minbq: fci__minbq
fci__minmq: fci__minmq
fci__cov: fci__cov
fci__rf: fci__rf
fci__intervals: fci__intervals
abra__kmers: abra__kmers
abra__mad: abra__mad
fix_mate_information__sort_order: fix_mate_information__sort_order
fix_mate_information__validation_stringency: fix_mate_information__validation_stringency
fix_mate_information__compression_level: fix_mate_information__compression_level
fix_mate_information__create_index: fix_mate_information__create_index
out: [ir_bams, covint_list, covint_bed]
BQSR_workflow:
run: BQSR/bqsr_workflow.cwl
in:
run_tools: run_tools
bams: ABRA_workflow/ir_bams
tmp_dir: tmp_dir
reference_fasta: reference_fasta
bqsr__nct: bqsr__nct
bqsr__rf: bqsr__rf
bqsr__knownSites_dbSNP: bqsr__knownSites_dbSNP
bqsr__knownSites_millis: bqsr__knownSites_millis
print_reads__nct: print_reads__nct
print_reads__EOQ: print_reads__EOQ
print_reads__baq: print_reads__baq
out: [bqsr_bams]