Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

WDL script is not copying the index files for the reference genome from its directory

  • The input json file has three inputs (reference, intervalBED, and BAMlist).
  • reference : Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
  • intervalBED: Sequencing_kits/Roche/SeqCap/interval_list.bed
  • BAMlist: Sequencing_data/ProjectA/BAM_files.list

  • In human reference directory, I have the following files: genome.fa and genome.fa.fai, genome.dict

  • WDL script is successfully copying the reference file from its directory and making a copy of it while creating a session for each run. But it fails to copy the "FASTA index file".

Is there any way, I can refer the index file in GATK command?

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Answers

  • NandaNanda CanadaMember
    Accepted Answer

    Hi WDL team, I figured it out, I mentioned them in the json file and called those variables in the task block. It worked for me.

  • ChrisLChrisL Cambridge, MAMember, Broadie, Moderator, Dev admin

    That's right - the task needs to specify all the files which need to be localized before execution, even if the command line itself doesn't refer to them.

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