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stjudecloud / workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.
MIT License
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Arriba #137

Closed adthrasher closed 3 months ago

adthrasher commented 7 months ago

Adding support for Arriba. The most controversial thing is likely to be the changes I made to the STAR defaults. Some are required to output chimeric alignments. Others are likely more debatable. The changes reflect the parameters that Arriba uses when running STAR.

adthrasher commented 6 months ago

@claymcleod - I don't think you need to review the Arriba changes, but I wanted to ping you for the STAR changes. I'm opting to change some parameters here to match Arriba recommendations. Most of the parameters relate to enabling chimeric alignment output, which I think we intended to enable previously. However, there are a couple that are more broadly applicable.

adthrasher commented 3 months ago

@a-frantz - I rebased from main. So this should contain all of the parameter renames. I've updated them in rnaseq-core as well. I think I've got it all clean now. I also migrated some setting changes out of STAR and into rnaseq-core. The only thing that should be left in STAR is the parameter to enable chimeric detection and output them into the BAM.