Is it possible to ensure VCF indices (and other secondary files) are localized to the same directory in WDL?

Former User of DNAx Community_18
Simple example:   input { File vcf File csi } command <<< bcftools view -r chr1 ~{vcf} >>>   this fails because the .csi file is not localized to the same dir. I think I can hack this with something like:   ln ~{vcf} in.bcf ln ~{csi} in.bcf.csi bcftools view -r chr1 in.bcf   but this is less than ideal. This might be a more general issue with WDL. There is some discussion here:   https://bioinformatics.stackexchange.com/questions/15197/how-do-i-force-cromwell-wdl-to-put-input-files-in-the-same-directory  

Comments

2 comments

Date Votes
  • Comment author
    Chai Fungtammasan DNAnexus Team

    I had the same question before, and what DNAnexus's engineering team recommend me is indeed to use softlink. The location of the file would be some random name folder, so it's not possible to predict them a head of time when we write the code.

    I would leave this thread open though in case anyone else has better trick to share.

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  • Comment author
    Former User of DNAx Community_18

    Thanks Chai.

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