I have a CWL file which has
bam file as one of the inputs and takes
bai file as secondary files. The script as
CommandLineTool works and gives results when run in cwl-runner.
cwlVersion: v1.0 class: CommandLineTool baseCommand: [python, degradation.py] inputs: annotation: type: File inputBinding: position: 2 prefix: -a bam: type: File inputBinding: position: 1 prefix: -n secondaryFiles: .bai
Now I would like to add this script as one of the steps in the workflow. How can this be done ?
cwlVersion: v1.0 class: Workflow inputs: ------ ------ outputs: alignment_out: type: File outputSource: star/star_bam steps: star: run: star.cwl in: --- ------- out: [star_bam] bam_indexing: run: index_bam.cwl in: bam: star/star_bam out: [bai] rna_degradation: run: degradation.cwl in: annotation: annotation bam: star/star_bam bai: bam_indexing/bai
expects secondaryFiles: .bai but source 'star_bam' does not include secondaryFiles. To fix, add secondaryFiles: .bai to definition of 'star_bam'.
star_bamis an output from the step
bai is an output from another step
In that case, how could
baibe given as an input(secondaryFile) to the step