GenotypeGVCF scatter wdl not parsing

[jsotobroad]

This wdl is failing to Build with this error - `Context initialization failed due to TypeError: Cannot read property 'i' of undefined.

Wdl can be found here - https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_dsde_workflows/GenotypeGVCFsScatterWf_170204.wdl

[jsotobroad]

It happens in this wdl as well - https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_dsde_workflows/HaplotypeCallerGvcfScatterWf_170204.wdl

It seems like its having trouble parsing this line interval_list = interval_file, in this call

  scatter (interval_file in scattered_calling_intervals) {

    # Generate GVCF by interval
    call HaplotypeCaller {
      input:
        input_bam = input_bam,
        input_bam_index = input_bam_index,
        interval_list = interval_file,
        gvcf_name = gvcf_name,
        gvcf_index = gvcf_index,
        ref_dict = ref_dict,
        ref_fasta = ref_fasta,
        ref_fasta_index = ref_fasta_index
    }
  }

The scatter value comes from Array[File] scattered_calling_intervals = read_lines(scattered_calling_intervals_list)

Something similar happens in the first wdl as well.

If I remove the interval_list = interval_file, line the wdl builds successfully

[sidoruka]

@jsotobroad , thanks so much for noticing!

We've created PR https://github.com/epam/pipeline-builder/pull/18 that hopefully fixes this.

[jsotobroad]

Thats awesome, thanks!

[sidoruka]

@jsotobroad , fixes are merged into dev and available for testing on http://pb.opensource.epam.com:10000/ (this is a demo app endpoint that is built from dev branch) Both scripts that you've provided seem to work fine now.

Could you please test it?

[jsotobroad]

These wdls are now working!

There are some other wdls in https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_dsde_workflows/ that are still failing to build but they seem to have the same issue described in https://github.com/epam/pipeline-builder/issues/15

[sidoruka]

Seems that these issues are fixed in the PRs that were merged recently. We've tested all scripts from the folder you've provided, looks good to my mind. Could you give it a try on http://pb.opensource.epam.com:10000/?

Also we linked these scripts into a demo application (TOOLS -> BROAD WDL EXAMPLES -> broad_dsde_workflows). You can load workflows visualization by clicking a wf item.

[jsotobroad]

That is awesome, it looks good! Having the example wdl in the tool section is really handy.