[WIP] add picklist support to config file #136
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
I'm going to merge this in to #130 so that I can work on the tests all together... |
ctb
added a commit
that referenced
this pull request
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]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Note: PR into #130
Addresses #132 by adding a
picklist:config file parameter that lets you subselect on genomes.TODO: