My question is about whether there exists any examples of how to create a workflow in CWL consisting of two steps:
- Create BWA indexes from input FASTA using BWA INDEX
- Pass indexes from step 1 to BWA MEM to perform an alignment
The issue I foresee is that BWA MEM in Step 2 expects a single reference FASTA as the command line input, and yet Step 1 creates a number of files which must be placed in the correct directory such that BWA MEM can access them. So, how does one cleanly pass the output of Step 1 into Step 2?