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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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Need to deprecate `merge_mafs` method of `update_cBioPortal_data.py` #38

Closed stevekm closed 3 years ago

stevekm commented 3 years ago

The merge_mafs method of update_cBioPortal_data.py ends up using a lot of memory some times, as pointed out by @nikhil . There are newer more efficient methods available as shown in tmb_workflow.cwl that can merge tables using merge-tables.cwl and should not use so much memory.

stevekm commented 3 years ago

another method that might be better would be to pre-save one of the maf's as sqlite so that values can be retrieved without loading everything in memory

stevekm commented 3 years ago

closing this since its not closing this until we need to address it