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thelovelab / tximport

Transcript quantification import for modular pipelines
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Fix for Salmon 0.14 num_targets -> num_valid_targets issue. #30

Closed roryk closed 5 years ago

roryk commented 5 years ago

This is the same gotcha as in bcbio/bcbio-nextgen#2843.

Fixes #29.

Test data to show this fixes the issue can be grabbed here: https://www.dropbox.com/s/d5325xe3weo8io2/tximport-example.tar.gz?dl=1

mikelove commented 5 years ago

Thanks Rory, I’ll pull this ASAP

roryk commented 5 years ago

Thanks Mike!

rob-p commented 5 years ago

Hi guys (@roryk & @mikelove), sorry for the unintended consequences of that naming change!

roryk commented 5 years ago

@rob-p No worries!

mikelove commented 5 years ago

I just bumped the version number so this is v1.13.3 in the devel branch.

roryk commented 5 years ago

Thanks, does this get updated on bioconductor, or does that only happen when there is a new official bioconductor release? I'm wondering how to update the bioconductor-tximport bioconda recipe so this fix gets pulled in.

mikelove commented 5 years ago

I'll push to release as well, and it should propagate in 1-2 days.

roryk commented 5 years ago

Great, thanks for the quick merge and fix Mike!

mikelove commented 5 years ago

Just pushed 1.12.1 which usually is available by ~1pm US East tomorrow.

roryk commented 5 years ago

Awesome 1.12.1 showed up on bioconductor today-- I updated the bioconda package so we should be good to go now. Thanks a bunch Mike!