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UCSC-Treehouse / pipelines

Makefiles to run dockerized pipelines used in Treehouse on a single sample
Apache License 2.0
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Use bam from umend for min-var call #16

Closed rcurrie closed 6 years ago

rcurrie commented 6 years ago

I've modified the pipeline's Makefile and fabfile to only preserve the bam output from umend and use that for min-var-call. Updated umend and docker as well (see separate pull request). This means the the bam will live under umend at the end of a treeshop run. e-t-k - note my hack to delete the locally pulled rnaseq bam - expediant for the moment to make this a smaller set of code change. Doing it 'right' means possibly breaking the Makefile or re-structuring the way backhaul works...

I've run this on the TEST sample and it works both in Makefile and Treeshop

hbeale commented 6 years ago

Sounds good to me.

rcurrie commented 6 years ago

@e-t-k Ok to merge? Or should I hold off till your done with your run, happy either way.

e-t-k commented 6 years ago

@rcurrie if you don't mind waiting until next week so i can have a chance to look at it that would be great. I'm swamped today with v6 stuff.

rcurrie commented 6 years ago

@e-t-k no problem, standing by.