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cwlVersion: v1.1
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
hints:
ResourceRequirement:
ramMin: 3000
inputs:
fastq_forward: File
fastq_reverse: File?
ref_fasta:
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
- .fai
threads:
type: int
default: 4
metadata: File?
sample_id: string
outputs:
out_fasta:
type: File
outputSource: bam2fasta/out_fasta
out_metadata:
type: File?
outputSource: metadata
steps:
bwa-mem:
in:
threads: threads
fastq_forward: fastq_forward
fastq_reverse: fastq_reverse
index_base: ref_fasta
out: [output]
run: bwa-mem.cwl
samtools-view:
in:
threads: threads
input_file: bwa-mem/output
out: [bam]
run: samtools-view.cwl
samtools-sort:
in:
input_bamfile: samtools-view/bam
threads: threads
out: [sorted_bam]
run: samtools-sort.cwl
bam2fasta:
in:
bam: samtools-sort/sorted_bam
fasta: ref_fasta
threads: threads
sample_id: sample_id
out: [out_fasta]
run: bam2fasta.cwl
|
