/
fastq_clean_pe.cwl
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/
fastq_clean_pe.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
requirements:
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/readgroup.yml
class: Workflow
inputs:
- id: input
type: ../../tools/readgroup.yml#readgroup_fastq_pe_file
- id: job_uuid
type: string
outputs:
- id: output
type: ../../tools/readgroup.yml#readgroup_fastq_pe_file
outputSource: emit_readgroup_fastq_pe_file/output
- id: sqlite
type: File
outputSource: json_to_sqlite/sqlite
steps:
- id: fastq_cleaner_pe
run: ../../tools/fastq_cleaner_pe.cwl
in:
- id: fastq1
source: input
valueFrom: $(self.forward_fastq)
- id: fastq2
source: input
valueFrom: $(self.reverse_fastq)
out:
- id: cleaned_fastq1
- id: cleaned_fastq2
- id: result_json
- id: emit_readgroup_fastq_pe_file
run: ../../tools/emit_readgroup_fastq_pe_file.cwl
in:
- id: forward_fastq
source: fastq_cleaner_pe/cleaned_fastq1
- id: reverse_fastq
source: fastq_cleaner_pe/cleaned_fastq2
- id: readgroup_meta
source: input
valueFrom: $(self.readgroup_meta)
out:
- id: output
- id: json_to_sqlite
run: ../../tools/json_to_sqlite.cwl
in:
- id: input_json
source: fastq_cleaner_pe/result_json
- id: job_uuid
source: job_uuid
- id: table_name
valueFrom: "fastq_cleaner_pe"
out:
- id: sqlite
- id: log