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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
doc: "samtools sort, sort given bam file"
requirements:
DockerRequirement:
dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
InitialWorkDirRequirement:
listing:
- $(inputs.input_fasta)
baseCommand: [samtools, faidx]
inputs:
input_fasta:
type: File
label: "Input fasta"
inputBinding:
position: 1
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
outputs:
indexed_fasta:
type: File
outputBinding:
glob: "$(inputs.input_fasta.basename)"
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
- .fai
stdout: stdout
stderr: stderr
stdout: samtools-sort-stdout.log
stderr: samtools-sort-stderr.log
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