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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. $\endgroup$
    – Roger V.
    Commented Jan 14, 2021 at 8:29
  • $\begingroup$ @Vadim the code does not reference RefFai or RefDict, only Ref. $\endgroup$
    – Greg Dougherty
    Commented Jan 21, 2021 at 22:31
  • $\begingroup$ I am talking about the wdl code: one must pass all the files explicitly to the task, even if they do not appear in the command line. Every task is run from a separate folder. $\endgroup$
    – Roger V.
    Commented Jan 22, 2021 at 6:28

2 Answers 2

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as for wdl version 1.0 (other versions untested)

you can pack your reference and related files into a struct:

struct Reference {
    File fasta
    File dict
    File fai
}

You will pass the Reference to your tasks instead of File. Inside your workflow/config define:

Ref example = {
    "fasta" : "reference.fasta",
    "fai" : "reference.fasta.fai",
    "dict" : "reference.dict"
}

Inside the task you just use the file want use by example.fasta.

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My hacktastic fix for this is to use basename to get the name of each file, then do

refName=`basename "${Ref}"`
ln -s "${Ref}" "$refName"

for each file. This puts aliases to each file in the executions dir, and then I pass "refName" to GATK rather than "${Ref}".

Not a good solution, but a solution

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