release 2.0 #225
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release 2.0 #225
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…cutoffs reformatted. configurations added to handle executable and database dependencies. k-mer counting (multiprocessing capable), normalization and embedding (multiple methods via TSNE and UMAP). external dependencies handled in external directory. utilities for archiving, unzipping, etc added in common directory. metagenome and mag classes to handle respective data. binning directory for multiple binning algorithms. docs directory containing jupyter notebooks with information about autometa as well as template python script for writing new modules ot plug in to autometa. Added projects folder as default location where autometa will place metagenome binning jobs. Added taxonomy folder for taxon assignment algorithms/utilities.
…quired options. updates to database handling and added timeit to main function calls.
…nomy() and changed logger for diamond to debug. utilities timeit now is INFO level logging. some 'f' string formatting for kmers and diamond logs (added comma thousand separators).
…noparallel arg to parallel so does GNU parallel disabled by default. updated config sections to reflect parameter change
…Updated coverage.py args and metagenome.py and autometa.py to reflect new args. added respective files under [files] section in default.config and metagenome.config files.
…r --out in coverage.py and moved return statement in taxon assignment in metagenome.py to reduce redundancy.
… binning respective to selected kingdom. Choices are bacteria and archaea. bugfix where environs were being placed under database section in config. added samtools and bedtools to environ checks (used in coverage calculations). Updated default config files respective to coverage calculations
📝🔥 Fix typos in autometa-bash-workflow
📝 Add legacy Autometa mention
This was
linked to
issues
Jan 27, 2022
…ntainer (#229) * 🎨🍏 Add optional output and logic to handle archaea input * 🎨🔥🍏 Remove unnecessary subworkflow for binning summary and binning. * 🎨🍏 Add working version of using either bacteria or archaea based on params.kingdom * 🎨🐛🍏 Add meta.cov_from_assembly = spades for mock data spades coverage channel * 🎨🍏🔥 Remove redundant code in autometa.nf channels and unused params line in binning_summary.nf * 🎨🍏 fixes #187 KMER sub-workflow * 🎨✅ Fix test for unclustered_recruitment.py * 🎨🐛🍏🐍 Re-write unclustered recruitment features table to output-features and main to output-main * 🎨🐍🐛 Incorrect cluster col usage in get_metabin_stats for binnin/summary.py * 🎨🍏 Rename bin_contigs.nf to binning.nf * 🎨🍏 Update tags for kmers, binning and recruitment * 🎨🐍 Update kmers main behavior so kmer pipeline may be run at multiple different stages * 🎨🍏 Update modules.config for new local kmer and binning processes * 🔥🍏 Fixes #163 * 🎨🐛🐍 Fix main logic for handling missing files for kmers * 🔥🐛 Remove added args in main logic of kmers.py * 🔥✅ Remove unnecessary import * 💚🔥🐛 Remove duplicat norm_df fixture in test_kmers.py * 🔥 Remove unused import in test_recursive_dbscan.py * ✅🎨🐍🍏 Add behavior to raise/handle 204 exit code for autometa-binning/binning.nf * ✅ Add test for raising a TableFormatError * 🍏 Add errorStrategy to binning.nf to ignore the 204 error * 🐍🎨 Add sys.exit(204) exit code when raising a BinninError or TableFormatError for recursive_dbscan.py * 🎨🍏🐍 Replace 0 exit code with 204 and add handling 204 exitcode in RECRUIT
chasemc
reviewed
Jan 31, 2022
chasemc
reviewed
Jan 31, 2022
🍏🎨 Alias CONTIG_COVERAGE to COVERAGE in autometa.nf
🍏🎨 Alias SPADES_KMER_COVERAGE to COV_FROM_SPADES in autometa.nf
🍏🎨 Change channel instantiations to 'idiomatic' method of chaining using set{...} method
* 🎨🐍🍏 Add errorStrategy for markers annotation if none pass cutoff thresholds * 🎨🐛🐍🍏 Place sys.exit(204) within main() * 🎨🐛🍏🐍 Exception handling from the if __name__ == '__main__' block does not raise the error code from the entrypoint. The sys.exit(204) message must be within main for the error code to be recognized by nextflow * 🎨🍏 alias LCA processes. add errorStrategy for 153 exitcode of embed_kmers.nf * 🎨✅🐛 Change error handling main test in test_recursive_dbscan.py
…of tmpdir for coverage calculations
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🎨 Change links from dev to main