Polishing for 1.5 release #13
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…e max_threads for each.
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #13 +/- ##
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+ Coverage 87.15% 88.10% +0.95%
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Files 5 5
Lines 179 185 +6
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+ Hits 156 163 +7
+ Misses 23 22 -1 ☔ View full report in Codecov by Sentry. |
MatthiasZepper
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Docker and Singularity images are broken...🥲 ...and fixed with updating to bookworm base images. |
| >### Performance Note | ||
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| >The decompression and compression used within umi-transfer is single-threaded, so to get the most reads per minute performance, see the [high performance guide](#high-performance-guide) | ||
| The tool requires three FastQ files as input. You can manually specify the names and location of the output files with `--out` and `--out2` or the tool will automatically append a `with_UMI` suffix to your input file names. It additionally accepts to choose a custom UMI delimiter with `--delim` and to set the flags `-f`, `-c` and `-z`. |
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Did we drop support for single-end mode? That would be only two input fastq:s. Mostly just curious
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Yes, we dropped that with version 1.0 See the Discontinued Previous Features section in the release notes. It was too much clutter with the previous code organization, which did not cleanly separate the iterators from the file i/o.
After the current refactoring, it would actually not be that hard to bring it back or also enable reading one input stream from stdin. But I also don't see that a singleton feature would be used frequently. Having paired reads to me seems to be the standard in recent years, and old data has no UMIs.
Co-authored-by: Johannes Alneberg <[email protected]>
This PR comprises the bug fix for the thread limit and additionally some polish for the upcoming 1.5 release:
--threadssetting to the output file writers, do a proper split.