Do not include file paths that don't exist in sampleSheet output

snystrom / cutNrun-pipeline

Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extensible elsewhere by changing configuration files.

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Open snystrom opened 4 years ago

snystrom commented 4 years ago

Issue is sampleSheet is currently pregenerated before the rules run. Some rules will fail because the experiment failed, and thus will have no reads.

Things to try

way to run validation at end of successful pipeline run and swap to NA if path is invalid
- Need to make sure this runs even with ctrl+C (maybe not.... but would be nice)