First of all, sorry for asking a question thats already been asked 100's of times, but I can't seem to find an answer that applies.
I'm trying to run an alignment task in docker using bwa-mem2, but for some reason, the reference inputs aren't loaded into the same directory.
The references are imported into the task as a struct containing the fasta/fai/dict and bwa indexes. Bwa uses the fasta file as "reference base" to localise the rest of the indexes, but for some reason cromwell puts the fasta/fai/dict in a different dir than the bwa indexes.
According to every answer, doc or example workflow I found, my approach should work, except it doesn't and I'm at a loss as to why.
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