+++ /dev/null
-cwlVersion: v1.1
-class: CommandLineTool
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
- DockerRequirement:
- dockerPull: curii/bwa-samtools-picard
- ShellCommandRequirement: {}
- ResourceRequirement:
- ramMin: 10000
- coresMin: 4
-
-hints:
- arv:RuntimeConstraints:
- outputDirType: keep_output_dir
-
-inputs:
- bam: File
- sample: string
-
-outputs:
- out:
- type: File
- outputBinding:
- glob: "*fixed.bam"
-
-baseCommand: samtools
-
-arguments:
- - fixmate
- - -O
- - "bam"
- - $(inputs.bam.path)
- - $(runtime.outdir)/$(inputs.sample).fixed.bam