Add binned quality option#97
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Readme update
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Note that the test bins match i100 as seen here https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009540 |
* bump base image, R, dada2-nf version * python deps updated from direct-requirements.txt * add wget to apt list * base pip, no pip3 on ubuntu24.04 * add uv, install python deps into virtualenv and manipulate PATH * require non-empty seqs in trimmed fastq * bump vsearch, infernal * Updating deps * Pin Docker Python deps for Python 3.10 --------- Co-authored-by: Daniel Hoogestraat <dhoogest@uw.edu>
- see benjjneb/dada2#2202 for versioning weirdness
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@crosenth I've bumped the dada2 version in this branch and have added a comment. Should be good to go for merge and release tag. |
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Adds conditional handling and tests for executing a binned quality score
learnErrorsas described here. To specify error bins, extend the dada2 params with a section containing:A test fixture with data from i100 mock community is added in test/i100_takara.
/cc @crosenth @nhoffman