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#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: CommandLineTool
doc: string
requirements:
DockerRequirement:
dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5
InitialWorkDirRequirement:
listing:
- $(inputs.input_fasta)
baseCommand: [bwa, index]
inputs:
input_fasta:
type: File
label: "input fasta file"
inputBinding:
position: 1
outputs:
indexed_fasta:
type: File
outputBinding:
glob: $(inputs.input_fasta.basename)
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
stdout: stdout
stderr: stderr
stdout: bwa-index-stdout.log
stderr: bwa-index-stderr.log
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