I have a workflow that starts with untarring a file into a directory. In the second step, I need one file from that directory as parameter
--genomeDir for my tool.
Currently this is solved like so:
star: run: ../tools/STAR.cwl in: index: tar/output fastq: [TUMOR_FASTQ_1, TUMOR_FASTQ_2] out: [output]
inputs: index: type: Directory
arguments: - valueFrom: $(inputs.index.path + "/ref_genome.fa.star.idx") position: 0 prefix: --genomeDir
This works, but seems unnecessarily complex, and it also puts a
prefix in the arguments. How do I pass the file directly from the workflow? I'm thinking something along the lines of
index: $((tar/output).path + "/ref_genome.fa.star.idx")
And while we're at it, what if I did want to parse this inside the tool cwl, how do I do it in the inputs?