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BD2KGenomics / toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
Apache License 2.0
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Add support for output file naming (resolves #57) #58

Closed wshands closed 7 years ago

wshands commented 7 years ago

Added support for basename for output file naming @jvivian

Fixed most comments in Thomas' pull request. The ones I did not: I believe the '-f' switch for docker tag has been deprecated (check with CJ) so I removed it; it also failed in my tests with the '-f' but worked without it I left the original code for getSampleName which split on a '.' to try an minimize side effects of code changes

jvivian commented 7 years ago

Thanks @wshands — I know you're on a time crunch, so contingent upon jenkins building successfully I'll merge this.

wshands commented 7 years ago

OK one thing is that with these changes I believe the wrapper will always remove the 'FAIL.' prefix, not sure if this is what we want...is it OK with you?

jvivian commented 7 years ago

OK one thing is that with these changes I believe the wrapper will always remove the 'FAIL.' prefix, not sure if this is what we want...is it OK with you?

That's what you want — the only possible conflict would be if a user submits a sample prepended with FAIL., in which case it would be stripped off.

wshands commented 7 years ago

OK I replaced strip with slice for new file name

jvivian commented 7 years ago

Thanks @tboser @wshands — I'll go ahead and merge, cherrypick this commit over to the release branch and push out a new release 3.1.2.