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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
baseCommand: [samtools, sort]
inputs:
threads:
type: int
default: 4
inputBinding:
prefix: -@
tmpfile:
type: string
default: sort.tmp
label: "Write temporary files to PREFIX.nnnn.bam"
inputBinding:
prefix: -T
output_bam:
type: string
default: aln.sorted.bam
label: "Write final output to FILENAME"
inputBinding:
prefix: -o
input_bamfile:
type: File
label: "Input bamfile"
inputBinding:
position: 1
outputs:
sorted_bam:
type: File
outputBinding:
glob: "$(inputs.output_bam)"
stdout: stdout
stderr: stderr
stdout: samtools-sort-stdout.log
stderr: samtools-sort-stderr.log
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