Containerize and Write CWL for Manta

[rhshah]

• available starting points:

  • https://hub.docker.com/r/cmopipeline/strelka2_manta
  • https://github.com/mskcc/tempo/blob/master/containers/strelka2_manta/Dockerfile
  • https://hub.docker.com/r/mgibio/manta_somatic-cwl/dockerfile
  • https://hub.docker.com/r/kfdrc/manta/dockerfile

• It also requires convertInversion.py script exposed.

• It requires samtools (for version look here: /opt/common/CentOS_7)

• Manta Version (look here: /opt/common/CentOS_7)

• Generate a docker file

• Write CWL accompanying the docker file

[rhshah]

This will require a little more re-thinking.

We have got Manta, But Manta is not like one script launch its a two script launch. We will need to write a wrapper. Thus might need to create a separate Manta Repository

[rhshah]

One thing left here is where we should run convertInversion.py, because it requires us to unzip the bgzip file and then use unzipped file to do the conversion.