search

mskcc / pluto-cwl

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

remove task failure suppression #72

Closed stevekm closed 2 years ago

stevekm commented 2 years ago

several workflow components have built-in suppression of failures using successCodes, such as here;

https://github.com/mskcc/pluto-cwl/blob/2742b41ab2946326e45c094cd5468d454b5e5b64/cwl/annotate-maf-wrapper.cwl#L10

I think this is responsible for some of the difficulty in diagnosing workflow failures, it should be removed.

For example, it was not until I removed this while debugging that I discovered further issues with open file handle limits being encountered; while this was enabled, the pipeline was failing with no descriptive error messages making it impossible to debug.

stevekm commented 2 years ago

this will get handled with future updates to remove facets from the workflow and run separately