cromwell 35 errors out on workflow

[ghost]

Hi!

I was directed to your workflow by my colleague Devin Locke and I was excited to finally find a well written WDL workflow that uses runtimes everywhere, rather than some assumed local state. I was also very happy to find that you provide an easily accessible and small test data set and input.json! I really appreciate the ease with which I could assemble a run for your workflow!

Unfortunately when I try and run the workflow on Cromwell 35 it errors out.

ERROR: Two or more calls or values in the workflow have the same name:

Declaration statement here (line 24, column 12):
    String basename = sub(sub(aligned_cram, "^.*/", ""), aligned_cram_suffix + "$", "")
           ^
      
Declaration statement here (line 96, column 12):
    String basename = sub(sub(aligned_cram, "^.*/", ""), aligned_cram_suffix + "$", "")
           ^

Thanks!
-Kaushik

[ghost]

Fixing the above duplicate name issue raises the error

ERROR: Call output not found: Call 'Extract_Reads' doesn't have an output 'output_cram' (line 38, col 34).
      input_cram = Extract_Reads.output_cram,
                                 ^
Options:
 - Add the output 'output_cram' to 'Extract_Reads'.
 - Modify the member access (on line 38) to use an existing output (current outputs of 'Extract_Reads': 'output_cram_index', 'output_splitters_bam', 'output_splitters_bam_index', 'output_discordants_bam', 'output_discordants_bam_index').

I'm getting closer ...

[ghost]

Adding the missing output port allows the workflow to run, yay!

[ernfrid]

Hi Kaushik,
Send my regards to Devin!
We've only recently updated to Cromwell 34, but I have noticed some incompatibilities with some of our old workflows. I must also admit that it's been quite some time since we've run the full workflow ourselves as we've been running very large cohorts in stages (Pre-Merge and then post-merge).

I did take a quick glance at the initial error and I would have thought what we had would work there, but it should be an easy fix.

Looks to me like the second error you hit should have matched this line in the Pre_Merge workflow:
https://github.com/hall-lab/sv-pipeline/blob/master/scripts/Pre_Merge_SV.wdl#L33