Create a CAVATICA OPC methylation-summary module app

[ewafula]

✨

[Required] Is this a new tool/workflow?

• Yes

[Required] Which tools/workflows would you like to update/add?

Provide software links and dockerPull location if applicable

• the methylation-summary module scripts and documentation here:
  • https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/update-methyl-summary/analyses/methylation-summary
• needs to wait until after PR #278 has been approved and merged.

[Required] What features (new params, inputs, outputs, etc) would you like to add to each?

Add reference files and test input locations if applicable

• all parameters, inputs, outputs, and software dependencies described in the methylation-summary module README
• all the module scripts include command-line options to enable easy implementation in CAVATICA

[Optional] How long do you think this work will take?

• For OPC v12 data release

[Optional] Who will complete this work?

• D3b bix-dev team

Ticket will be considered resolved either by a successful PR with updated release if applicable, or a simple denial of the request backed by a good reason

[sickler-alex]

Are the v12 data for this ready or should I just test the workflow with the v11 data, once I'm ready to start testing?

[jharenza]

You can work with v11 - @zhangb1 will be processing the v12 data soon

[sickler-alex]

Where will this be run? @yuankunzhu seems to think that this will be included in the monthly process which is run by an Airflow DAG. If that's the case, then we can just use the shell script that already exists to run this module. Do we need to run this on Cavatica or as a cwl workflow?

[sickler-alex]

Separate from my question above, I built a docker for this module to run it within the workflow since the current OPC docker is using an our of date R version. Once it's ready, where should it stay? I have the Dockerfile in the module and I uploaded the docker image to my docker hub so I can test it on Cavatica. The docker image will have to move to SBG's hosted docker repo since you can only download a docker image a certain number of times before you need a paid dockerhub account.

[ewafula]

@sickler-alex, hold to this until when ticket #478 is completed. These changes are needed for v12 MTP methylation tables.

I will update the module on your PR #307 branch to avoid multiple merges.

[jharenza]

This is no longer needed.