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bwa_pe.cwl
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bwa_pe.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/readgroup.yml
- class: StepInputExpressionRequirement
inputs:
- id: job_uuid
type: string
- id: reference_sequence
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .fai
- .pac
- .sa
- ^.dict
- id: readgroup_fastq_pe
type: ../../tools/readgroup.yml#readgroup_fastq_pe_file
- id: thread_count
type: long
outputs:
- id: bam
type: File
outputSource: bwa_pe/OUTPUT
- id: sqlite
type: File
outputSource: merge_sqlite/destination_sqlite
steps:
- id: fastqc1
run: ../../tools/fastqc.cwl
in:
- id: INPUT
source: readgroup_fastq_pe
valueFrom: $(self.forward_fastq)
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc2
run: ../../tools/fastqc.cwl
in:
- id: INPUT
source: readgroup_fastq_pe
valueFrom: $(self.reverse_fastq)
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc_db1
run: ../../tools/fastqc_db.cwl
in:
- id: INPUT
source: fastqc1/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_db2
run: ../../tools/fastqc_db.cwl
in:
- id: INPUT
source: fastqc2/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_basicstats_json
run: ../../tools/fastqc_basicstatistics_json.cwl
in:
- id: sqlite_path
source: fastqc_db1/OUTPUT
out:
- id: OUTPUT
- id: bwa_pe
run: ../../tools/bwa_record_pe.cwl
in:
- id: fasta
source: reference_sequence
- id: fastq1
source: readgroup_fastq_pe
valueFrom: $(self.forward_fastq)
- id: fastq2
source: readgroup_fastq_pe
valueFrom: $(self.reverse_fastq)
- id: fastqc_json_path
source: fastqc_basicstats_json/OUTPUT
- id: readgroup_meta
source: readgroup_fastq_pe
valueFrom: $(self.readgroup_meta)
- id: thread_count
source: thread_count
out:
- id: OUTPUT
- id: bam_readgroup_to_json
run: ../../tools/bam_readgroup_to_json.cwl
in:
- id: INPUT
source: bwa_pe/OUTPUT
- id: MODE
valueFrom: "lenient"
out:
- id: OUTPUT
- id: readgroup_json_db
run: ../../tools/readgroup_json_db.cwl
scatter: json_path
in:
- id: json_path
source: bam_readgroup_to_json/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: log
- id: output_sqlite
- id: merge_readgroup_json_db
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: readgroup_json_db/output_sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: merge_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: [
fastqc_db1/OUTPUT,
fastqc_db2/OUTPUT,
merge_readgroup_json_db/destination_sqlite
]
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log