Excluding stages not handled properly

umccr / umccrise

:snake: DRAGEN Tumor/Normal workflow post-processing

https://umccr.github.io/umccrise/

MIT License

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Excluding stages not handled properly #135

Closed pdiakumis closed 1 year ago

pdiakumis commented 1 year ago

Using -E multiqc also excludes others stages due to https://github.com/umccr/umccrise/blob/fe1ab589ed3a504a3b93c8fadac72e1b00b94ccb/umccrise/__init__.py#L473 Need to see if we can get away with just specifying multiple stages to include.

Slack thread: https://umccr.slack.com/archives/C025TLC7D/p1680740277790899?thread_ts=1680137962.285599&cid=C025TLC7D

pdiakumis commented 1 year ago

That workaround with the explicit inclusion of multiple stages sans multiqc ended up working fine. -- Will not implement a proper fix for this since we're moving on.