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alignment_prep.cwl
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alignment_prep.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
job_uuid: string
input_bam: File
outputs:
time_metrics_from_bam_to_fastq:
type: File
outputSource: bam_to_fastq/time_metrics
output_readgroup_lines:
type: string[]
outputSource: bam_to_fastq/output_readgroup_lines
output_readgroup_names:
type: string[]
outputSource: bam_to_fastq/output_readgroup_names
output_fastq1:
type: File[]
outputSource: bam_to_fastq/output_fastq1
output_fastq2:
type: File[]
outputSource: bam_to_fastq/output_fastq2
steps:
get_readgroup_info:
run: ../../tools/harmonization/get_readgroup_name.cwl
in:
bam: input_bam
out: [readgroup_lines, readgroup_names]
bam_to_fastq:
run: ../../tools/harmonization/bam_to_fastq.cwl
in:
job_uuid: job_uuid
readgroup_lines: get_readgroup_info/readgroup_lines
readgroup_names: get_readgroup_info/readgroup_names
filename: input_bam
out: [output_readgroup_lines, output_readgroup_names, output_fastq1, output_fastq2, time_metrics]