1 #!/usr/bin/env cwl-runner
9 InitialWorkDirRequirement:
11 - $(inputs.bam_sorted)
17 dockerPull: quay.io/biocontainers/samtools:1.14--hb421002_0
19 baseCommand: ["samtools", "index"]
21 - valueFrom: -b # specifies that index is created in bai format
26 doc: sorted bam input file
35 format: edam:format_2572 # BAM
37 glob: $(inputs.bam_sorted.basename)
40 edam: https://edamontology.org/
42 - https://edamontology.org/EDAM_1.18.owl