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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
baseCommand: [bwa, mem]
inputs:
threads:
type: int
label: "number of threads"
default: 4
inputBinding:
prefix: -t
output_sam:
type: string
label: "sam file to output results to"
default: "out.sam"
inputBinding:
prefix: -o
group_header_line:
type: string?
label: "read group header line such as '@RG\tID:foo\tSM:bar'"
inputBinding:
prefix: -R
index_base:
type: File
label: "fasta file for index basename"
inputBinding:
position: 1
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
fastq_forward:
type: File
label: "input fastq file to map (single-end or forward for pair-end)"
inputBinding:
position: 2
fastq_reverse:
type: File?
label: "input fastq file to map (reverse for pair-end)"
inputBinding:
position: 3
outputs:
output:
type: File
outputBinding:
glob: "$(inputs.output_sam)"
stdout: stdout
stderr: stderr
stdout: bwa-mem-stdout.log
stderr: bwa-mem-stderr.log
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