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unix_align_workflow.cwl
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unix_align_workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
- id: bam_path
type: File
outputs:
- id: merged_bam
type: File
outputSource: merge/MERGED_OUTPUT
steps:
- id: bamtoreadgroup
run: ../../tools/unix/unix_bamreadgroup_cmd.cwl
in:
- id: bam_path
source: bam_path
out:
- id: output_readgroup
- id: bamtofastq
run: ../../tools/unix/unix_bamtofastq_cmd.cwl
in:
- id: bam_path
source: bam_path
out:
- id: output_fastq1
- id: output_fastq2
- id: align
run: ../../tools/unix/unix_align_cmd.cwl
scatter: [align/fastq1_path, align/fastq2_path, align/readgroup_path]
scatterMethod: "dotproduct"
in:
- id: fastq1_path
source: bamtofastq/output_fastq1
- id: fastq2_path
source: bamtofastq/output_fastq2
- id: readgroup_path
source: bamtoreadgroup/output_readgroup
out:
- id: output_bam
- id: merge
run: ../../tools/unix/unix_merge_cmd.cwl
in:
- id: INPUT
source: align/output_bam
- id: OUTPUT
source: bam_path
valueFrom: $(self.basename)
out:
- id: MERGED_OUTPUT