Release PR for 2.0.0 #410
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Release PR for 2.0.0 #410
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Fix param arg_amrfinderplus_name
Important! Template update for nf-core/tools v2.14.1
Fix RGI fail
…GC + taxonomy merge due to wrong sample names
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
jasmezz
commented
Aug 6, 2024
jasmezz
commented
Aug 6, 2024
jasmezz
commented
Aug 6, 2024
jasmezz
commented
Aug 6, 2024
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
adamrtalbot
approved these changes
Aug 8, 2024
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Congrats on a herculean effort. Looks like a very good job.
I've left some comments about improvements you could make but none of these are blocking I would hate for a release of this magnitude to get delayed for minor code stuff. It is readable and maintainable. I assume it works so it's good to go!
| # grab the unique sample names from the taxonomy table | ||
| samples_taxa = taxa_df['sample_id'].unique() | ||
| # for every sampleID in taxadf merge the results | ||
| for sampleID in samples_taxa: |
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This is a bit too much looping over a Pandas DataFrame for my liking. I would consider using a vector operation if you can for memory and speed reasons.
Since this looks pretty quick I don't think it's critical but it may slow down on really large data.
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@Darcy220606 Comment for you on the taxa merge script – you might come back to this for 2.1?
| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: // This script is bundled with the pipeline, in nf-core/funcscan/bin/ |
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Template for what do you mean? 😶
…h database directroy
Fix hamronization fargene input
luispedro
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Aug 21, 2024
Big change is adding GROOT support Full Changelog: - argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot - GROOT support is via the `GrootNormalizer` (for use in python scripts) and the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters in the CLI. Other ----- - `__version__` attribute added to the package (accessible as `argnorm.__version__` or `argnorm.lib.__version__`) - Use atomic writing for outputs (https://github.com/untitaker/python-atomicwrites/tree/master) funcscan integration -------------------- - argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/ - argNorm will also be available on the funcscan pipeline: nf-core/funcscan#410 DB harmonisation ---------------- - SARG db link was changed in `crude_db_harmonisation` to https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta as old link (Galaxy instance, http://smile.hku.hk/SARGs) is down - RGI outputs in `crude_db_harmonisation` are concatenated so frequencies of `perfect`, `strict`, and `loose` hits can be calculated from concatenated file
Database preparation docs improvements
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Added--metaparameter to default for Bakta, with singlemode optional. (by @jasmezz)--pfam2go,--rre, and--tfbs. (reported by @Darcy220606, added by @jasmezz)Fixedhamronization/summarizemodule. (by @Darcy220606)tests/from.gitignore. (by @Darcy220606)arg_amrfinderplus_name. (by @m3hdad)DependenciesDeprecatedPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).