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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Automatically download and extract the GATK jar #57

Open abhi18av opened 2 years ago

abhi18av commented 2 years ago

We should consider adding a process which automatically downloads the GATK-3.8.0 using the public URL 

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.

This has some overlap with https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54