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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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create mini test bam files, standardized mini test maf files #50

Closed stevekm closed 3 years ago

stevekm commented 3 years ago

Some of the test cases for pluto take a very long time to run, for example the "1 maf" test case for workflow_with_facets.cwl takes about 30min on its own.

To help avoid some of these long execution times for test cases we have started using small dummy maf files as inputs in some test cases. However we do not have an equivalent for .bam files.

We should come up with some tiny .bam files that can be used in conjunction with the .maf files, which should be standarized, throughout the test cases to speed up execution and aid development.

stevekm commented 3 years ago

I started this in /juno/work/ci/helix_filters_01/fixtures/demo, need to finish updating it to include Facets data in the bam files, also need to save the Makefile I used for scripted demo sample generation somewhere in the repo

stevekm commented 3 years ago

this is implemented in dev and in the new msi branch, will merge to master soon