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Bump version of umi-tools to 1.14 #2971
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MatthiasZepper
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Trying editing the contains string, based on looking at the output of the CI tests
Bwa has changed to require a meta on the genome channel, which was part of the issue. I think I have now fixed that. My local configuration is failing to pull files to run the tests. Umitools dedup does not seem to be actually testing any of the output files though for md5 or presence of anything from the log file. |
SPPearce
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Mar 7, 2023
Update test.yml, based on docker output.
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matthdsm
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Mar 9, 2023
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After almost two years without updates, versions 1.13 and 1.14 of umi-tools were released early March 2023.
Those new versions comprise for example a speed-up for read pair mate writing. This improves performance for transcriptome alignments greatly (Time to run is reduced from 5 hours to 4 minutes) and is thus most anticipated for the RNA-seq pipeline.
Accordingly, I have also changed the process labels. Since
umi-tools
is not multithreaded, in particular process medium seemed like a waste of CPU.Also, the new
--umi-separator
command toumi-tools extract
will be beneficial. So far only available forumi-tools dedup
, so we had to stick to underscores as separator, although Illumina's bclconvert imposes a semicolon.PR checklist
versions.yml
file.label
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware