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Bump version of umi-tools to 1.14 #2971

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merged 12 commits into from
Mar 9, 2023

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MatthiasZepper
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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 to umi-tools extract will be beneficial. So far only available for umi-tools dedup, so we had to stick to underscores as separator, although Illumina's bclconvert imposes a semicolon.

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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@SPPearce
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SPPearce commented Mar 7, 2023

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 SPPearce marked this pull request as ready for review March 9, 2023 09:01
@SPPearce SPPearce mentioned this pull request Mar 9, 2023
@SPPearce SPPearce added this pull request to the merge queue Mar 9, 2023
Merged via the queue into nf-core:master with commit 6d9c7e4 Mar 9, 2023
@MatthiasZepper MatthiasZepper deleted the umi-tools_bump1.14 branch March 9, 2023 14:42
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3 participants