BSQR on RNA-seq data : error to find reference index file
I use GATK 4.0.3 to discover variant in SeaBass. When I use BaseRecalibrator alone with one file, it did the job. But when I use it in a wdl script using scatter-gather BaseRecalibrator don't found the reference fasta index file in the folder. But in this folder there is the fasta file and the fasta index file. My script is adapted from the RNA-seq GATK best practices (https://software.broadinstitute.org/gatk/documentation/article?id=4067).
Do you have any idea why it doesn't work when it is include in a wdl script using scatter-gather?