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mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools
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Containerize and write CWL for GATK3 PrintReads #15

Closed rhshah closed 5 years ago

rhshah commented 5 years ago

Tool: GATK3 PrintReads Location: https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.3-0-g37228af Version: 3.3.0

rhshah commented 5 years ago

Try GATK 4

allanbolipata commented 5 years ago

If you need it, this is the Dockerfile we use with Conpair which contains GATK 3.8: https://github.com/mskcc/vaporware/blob/master/containers/conpair/Dockerfile

I will add the older version with 3.3.0 anyway so you can have it ready, but GATK 4 is easily available in https://hub.docker.com/r/broadinstitute/gatk/tags?page=1.

allanbolipata commented 5 years ago

I have made the container for 3.3.0, located here https://hub.docker.com/r/mskcc/gatk

Also it's in feature/gatk_3.3.0 branch

shalabhsuman commented 5 years ago

I am assuming its safe to use the GATK4 image directly from GATK official Docker-Hub repo rather than building our own GATK image using a dockerfile. Correct?

shalabhsuman commented 5 years ago

The module for BQSR has been renamed to ApplyBQSR in GATK4 and all the parameters have been renamed as well.

rhshah commented 5 years ago

I think we should discuss these in the planning meeting before we change anything, from what you are describing @shalabhsuman looks like lot has changed, if that is the case lets build right now things for GATK 3.3.0 with PrintReads

shalabhsuman commented 5 years ago

continuing with GATK4..Moving this to #32