Open abhi18av opened 2 years ago
We should consider adding a process which automatically downloads the GATK-3.8.0 using the public URL
GATK-3.8.0
https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
And then unzip it via tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 and pass on the resultant GenomeAnalysisTK.jar through all processes.
tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
GenomeAnalysisTK.jar
This has some overlap with https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54
We should consider adding a process which automatically downloads the
GATK-3.8.0
using the public URLAnd then unzip it via
tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
and pass on the resultantGenomeAnalysisTK.jar
through all processes.This has some overlap with https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54