Qc workflow

[murphycj2]

Not nearly ready to merge yet, but let's use this as a starting point. Do you guys have time tomorrow to go over the requirements in https://github.com/msk-access/qc_generation/issues/3?

What I did:

• added picard and waltz modules (just a basic framework).
• the pipeline expects one BAM file as input. So this workflow needs to be run separately for each type of bam file.

I have many questions:

• do we want these QC metrics for pool A and pool B separately?
• do we have a file containing the baits?
• picard tools expects the bed file to contain the SAM-like header. Do we have files like that somewhere? I am not sure if waltz expects a simple bed file or not.
• is there better documentation for waltz than what is here? https://github.com/mskcc/Waltz
• how are we processing the all output files? do you have scripts to process it all further?
• will this be a workflow by itself or will it be a sub-workflow for something else? If the latter, can you help me understand why it is in its own repo?

[rhshah]

Here are my comments:

• Yes, pool A and pool B will be separate, but that is just a bed file change.
• I am not sure I understand this, but here are the bed files:
  • /work/access/production/resources/msk-access/current/regions_of_interest/current/MSK-ACCESS-v1_0-probe-A.sorted.bed
  • /work/access/production/resources/msk-access/current/regions_of_interest/current/MSK-ACCESS-v1_0-probe-B.sorted.bed
• @ionox0 you might have an interval file, compatible with Picard tools. But if not it should be easy to generate using /work/access/production/resources/reference/current/Homo_sapiens_assembly19.fasta. For Waltz, it expects a regular bed file.
• Documentation of Waltz is not that great, @ionox0 has been working on improving it but not sure where he is in that. But you can ask @ionox0 any question you have.
• This repo is for the bigger workflow to run the Quality Control, so what you wrote is a sub-workflow, probably adding it to cwl_subworkflows might make more sense.

[murphycj2]

@rhshah ok i'll add it to the cwl_subworkflow and close this pr