search

mskcc / pluto-cwl

CWL workflows for helix filter scripts
1 stars 6 forks source link

need to output per-sample portal maf files #79

Closed stevekm closed 2 years ago

stevekm commented 2 years ago

We need to output .maf files for each sample after applying portal filters.

Right now, we create these files here; https://github.com/mskcc/pluto-cwl/blob/2742b41ab2946326e45c094cd5468d454b5e5b64/cwl/portal-workflow.cwl#L381-L399

However, we are immediately concat'ing them into a single portal data_mutations_extended.txt file.

We need to output these files individually as well for use in downstream workflow (e.g. samples fillout workflow)

Also, we need to output these files in an array or record format that will keep them associated with their sample ID's for easier identification. This may require extra steps to be implemented in the workflow.

This is a requirement for implementation of automated samples fillout workflow implementation

stevekm commented 2 years ago

@allanbolipata

stevekm commented 2 years ago

closing this for now

instead, maf_filter was applied inside the samples fillout index workflow, so that muts.maf files input there can be filtered down to cBioPortal equivalents