3 label: Realigning fastqs and converting output to bam
5 arv: "http://arvados.org/cwl#"
6 cwltool: "http://commonwl.org/cwltool#"
10 dockerPull: curii/bwa-samtools-picard
11 ShellCommandRequirement: {}
17 arv:RuntimeConstraints:
18 outputDirType: keep_output_dir
36 stdout: $(inputs.sample).bam
52 - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
68 - $(inputs.sample).sorted.bam