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cwlVersion: v1.1
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
hints:
ResourceRequirement:
ramMin: 3000
inputs:
ref_fasta:
type: File
fastq_forward:
type: File
fastq_reverse:
type: File?
threads:
type: int
default: 4
outputs:
out_fasta:
type: File
outputSource: fastq2fasta/out_fasta
steps:
bwa-index:
in: {input_fasta: ref_fasta}
out: [indexed_fasta]
run: bwa-index.cwl
samtools-faidx:
in: {input_fasta: bwa-index/indexed_fasta}
out: [indexed_fasta]
run: samtools-faidx.cwl
fastq2fasta:
in:
fastq_forward: fastq_forward
fastq_reverse: fastq_reverse
ref_fasta: samtools-faidx/indexed_fasta
threads: threads
out: [out_fasta]
run: fastq2fasta.cwl
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