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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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Security update: Store downloaded bams in primary instead of downstream #23

Closed e-t-k closed 5 years ago

e-t-k commented 5 years ago

With this change, no bam is ever downloaded to the downstream hierarchy. Instead, QC bam is downloaded to primary/derived. Runs correctly on the TEST sample provided.

Incidentally also fixes #19 with update of variant input file path.

e-t-k commented 5 years ago

@rcurrie

manually verifying that it reflects what actually showed up

Yep, I checked the methods.json files generated by my test samples and the outputs were what I expected (or input in the case of variants). (And correctly represented the actual files as downloaded.)

Thanks!