This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
WDL script is not copying the index files for the reference genome from its directory
- The input json file has three inputs (reference, intervalBED, and BAMlist).
- reference : Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
- intervalBED: Sequencing_kits/Roche/SeqCap/interval_list.bed
In human reference directory, I have the following files: genome.fa and genome.fa.fai, genome.dict
WDL script is successfully copying the reference file from its directory and making a copy of it while creating a session for each run. But it fails to copy the "FASTA index file".
Is there any way, I can refer the index file in GATK command?