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I have a cromwell task that, among other variables, takes these three variables:

   File Ref             # Reference genome fasta
   File RefFai          # Reference Genome index
   File RefDict         # Reference Dictionary

While all three files make it into the task's "inputs" directory, they end up in different sub-directories of inputs:

ME $ find inputs
inputs

inputs/-181926642
inputs/-181926642/Sample.vcf.bgz.tbi
inputs/-181926642/Sample.vcf.bgz
inputs/-1548908437
inputs/-1548908437/GCA_000001405.15_GRCh38_no_alt_short_headers_nonACTG_to_N.dict
inputs/44588251
inputs/44588251/GCA_000001405.15_GRCh38_no_alt_short_headers_nonACTG_to_N.fa
inputs/44588251/GCA_000001405.15_GRCh38_no_alt_short_headers_nonACTG_to_N.fa.fai

Which means that when I call GATK and pass it the path to the .fa file, it gets rather cranky that the .dict file isn't in the same directory.

How do I force cromwell to put all three files in the same directory?

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  • $\begingroup$ We did have a similar problem and there is a solution to it... however, I have hard time recalling it, sinc eit was a while ago (and we abandoned WDL). Perhaps you could paste the code for the task, which would make it easier to see, if anything is missing. $\endgroup$ – Vadim Jan 14 at 8:29

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