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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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fillout maf needs to use updated MafWriter to ensure Amino_Acid_Change column is present #116

Closed stevekm closed 1 year ago

stevekm commented 1 year ago

The Amino_Acid_Change column is missing from some fillout output maf files, because not all files get run through the maf_filter.py script, which was previously responsible for adding the Amino_Acid_Change column

https://github.com/mskcc/helix_filters_01/blob/08c059305a810ba704ed492a41d46fac10d023fd/bin/maf_filter.py#L69

need to update the fillout methods to make sure a Maf Writer method is used to include this column in the output in all case.

stevekm commented 1 year ago

need to use the maf2portal script entrypoint https://github.com/mskcc/helix_filters_01/blob/08c059305a810ba704ed492a41d46fac10d023fd/tests/test_update_cBioPortal_data.py#L408

stevekm commented 1 year ago

Looks like this is already added here https://github.com/mskcc/pluto-cwl/blob/2e1a01a788126f2901ffecc92a48fcbcb81776e1/cwl/samples_fillout_workflow.cwl#L709

not able to replicate missing column in test datasets