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?