GATK4 branch does not require separate Picard

CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

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GATK4 branch does not require separate Picard #14

Closed jdwheaton closed 3 years ago

jdwheaton commented 4 years ago

The GATK4 jar has all of the Picard tools integrated, so it is no longer necessary to include a separate jar for Picard in the docker image nor to use the old command syntax which differs from the new GATK4 style.

I have made these changes in a local repository and can submit a PR if you'd like.

pditommaso commented 4 years ago

Nice! A PR is very welcome.

jdwheaton commented 4 years ago

No problem.

Solved in #15

pditommaso commented 3 years ago

Merged. Thanks again!