Use GATK4 integrated Picard

CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Mozilla Public License 2.0

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Closed jdwheaton closed 4 years ago

jdwheaton commented 4 years ago

Edited and tested main.nf to use Picard tools packaged within GATK4.

Modified Dockerfile-base to no longer package a separate Picard jar, NOT TESTED.

pditommaso commented 4 years ago

Thanks for this PR and sorry for the very late reply.

Does this mean that we can now run this pipeline with the latest GATK executable?

Yes, I've merged manually the gatk4, dsl2 version and this patch.

pditommaso commented 4 years ago

See 5241d01.