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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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fix source of input bam in the methods.json file for variant calling #19

Closed e-t-k closed 5 years ago

e-t-k commented 6 years ago

Thanks @hbeale for spotting this.

The methods.json for variants still claims the bam is coming from ucsc_cgl-rnaseq-cgl-pipeline when instead it is actually coming from ucsctreehouse-bam-umend-qc - update the code here with correct hash.

We should probably also retroactively correct the outputs from this version as the line; can detect by the line's change from sorted.bam to sortedByCoord.md.bam:

https://github.com/UCSC-Treehouse/pipelines/commit/dca77ed4987640ef949cde0aeaf50bc49a3d0364#diff-65218180447789ae9b6a89838c1966c9L485

rcurrie commented 6 years ago

master's Makefile still has the incorrect variant on the expression vs. qc bam. Looks like there have also been some other changes to treeshop so I'm hesitant to do the fixes. @aglyle or @e-t-k do you want to update and remove the other branches or I can if there are no other changes. Not exactly sure what katrina et. al. are running - hopefully not master...

rcurrie commented 6 years ago

@aglyle @e-t-k Ignore - the master Makefile is pulling from qc for variants...brain toast from dna nexus hacking...time to make dinner...