[MRG] Change column names in intermediate CSVs. #133
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Jan 17, 2022
) * rename rule to sourmash_prefetch_wc * start using {outdir}/genomes/ * swizzle up config to allowprivate_databases and genbank_databases, etc. * more progress: copying private genomes around * combine listing private and genbank genomes - seems to work\! * simplify the ListGenomes stuff * it's aliiiiiiiive * remove genbank accession requirement * remove genbank from most filenames, rules * rename minimap to mapping; add clean_gather * updated to properly (?) use checkpoints throughout * tests pass locally * fix typo * add the beginnings of testing for private databases * getting started * update all the things * [MRG] Change column names in intermediate CSVs. (#133) * change column names * remove old notebooks * fix mistake * comments etc. * remove glob pattern, configure genbank_cache * remove 'process' command * check for old config file params * add important comment * actually remove 'process' * check for 'database_taxonomy' instead of 'taxonomies' * add trailing / in Makefile * add default taxonomies file to system.conf * fix test files * fix conf-private.yml * start of doc/ subdirectory * initial commit * add badge * compleat first draft * minor corrections * spell check * add picklists into the config (#136) * fix 'taxonomies' in test config; check that it's a list * add comment * swipe from #97 * swipe getting started from #97 * update! * Apply suggestions from Taylor's docs review Co-authored-by: Taylor Reiter <[email protected]> * more update in re taylor's suggestions * more more update * even more update * more update * more update * fix help output for CLI * configure mkdocs * clean it out * update gitignore * add some figures * upd * more figure adjustment * add badges * simplify to single sourmash_dtabases; use 'local' instead of 'private' * update to 'local' instead of 'private' * fix extra backquote * more fix? * fix formatting * add tax test * add test for picklist * switch SRR5950647_subset over to use local_databses_info 🎉 * cleanup & commenting * add missing file Co-authored-by: HackMD <[email protected]> Co-authored-by: Taylor Reiter <[email protected]>
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Note: PR into #130
Change
ncbi_tax_nametodisplay_nameandacctoidentthroughout.