Feature/seperate out msi and tmb steps

mskcc / pluto-cwl

CWL workflows for helix filter scripts

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Feature/seperate out msi and tmb steps #104

Closed stevekm closed 1 year ago

stevekm commented 2 years ago

opening PR to track changes :)

stevekm commented 2 years ago

I merged in the latest dev also

stevekm commented 2 years ago

I merged in the latest dev again, this helps a little with testing, looks like test_workflow_with_facets.py is having issues with the new data_clinical_sample.txt file outputs. Need to double check this.

also can use a testing command like this on terra now;

$ CWL_ENGINE=Toil TMP_DIR=/fscratch/tmp LARGE_TESTS=T PRINT_TESTNAME=T INTEGRATION_TESTS=T make parallel-test-log

stevekm commented 2 years ago

Oh it looks like the order of the columns in data_clinical_sample.txt is now reversed for TMB and MSI columns but thats not a big deal so I will try to just update the test cases for this change.