fix: use spooker available in ccbrpipeliner module - Githubissues

CCBR / XAVIER

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

https://ccbr.github.io/XAVIER/

MIT License

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fix: use spooker available in ccbrpipeliner module #110

Closed kelly-sovacool closed 3 months ago

kelly-sovacool commented 3 months ago

Changes

Rather than having a copy of spooker and jobby in every pipeline, we're making them available in the ccbrpipeliner module.

As long as the module is loaded before launching xavier, these commands will be available.

Issues

NA

PR Checklist

(~Strikethrough~ any points that are not applicable.)

[x] This comment contains a description of changes with justifications, with any relevant issues linked.
~[ ] Update docs if there are any API changes.~
~[ ] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/~

kelly-sovacool commented 3 months ago

@samarth8392 this can be copied almost verbatim for ESCAPE, all you have to change is the correct pipeline name for spooker.