docs(cli): fix stale options, defaults, and examples in pgatk-cli.md#106
Conversation
Cross-checked every documented command/option against pgatk/commands/*.py. Fixes: - generate-decoy: rewrite the help block - it listed mostly invented short flags (-i, -o, -l, -n, -x, -w, -t, -b, -m) and two options (--cleavage_sites, --anti_cleavage_sites) that do not exist on the click command; correct flags are -in/-out/-e/-d/-s and the new --min_peptide_length/--max_peptide_length/--keep_target_hits options. - ensembl-downloader: remove -l/--list_taxonomies (no such option) and the example using it; add the real -en/--ensembl_name, --grch37, and --url_file options. - cosmic-downloader: add -P/--products and --url_file options. - cbioportal-downloader: add -th/--multithreading and --url_file options. - ncbi-downloader: add --grch37, --generate-transcripts, --generate-cds. - vcf-to-proteindb: -c/--config_file is optional (was listed Required); --exclude_consequences default includes regulatory_region_variant; the "parameters to change for non-ENSEMBL sources" note referred to --transcript_index/--consequence_index which do not exist - corrected to --transcript_str/--consequence_str/--biotype_str; -w default is cpu_count(), not 1. - dnaseq-to-proteindb: -c/--config_file is optional; --num_orfs default is 3 (matches click help string and ensembl_config.yaml). - cosmic-to-proteindb cell-line example: --filter_column 'Sample name' is the v2 column name; v103 uses SAMPLE_NAME. - Fix broken intra-page anchor #downloading-ncbi--clinvar-data -> #downloading-ncbi-clinvar-data (mkdocs slug normalizes slash to nothing). mkdocs build now produces zero warnings from user-facing pages (remaining warnings are in docs/plans/, which is historical content).
Qodo reviews are paused for this user.Troubleshooting steps vary by plan Learn more → On a Teams plan? Using GitHub Enterprise Server, GitLab Self-Managed, or Bitbucket Data Center? |
|
Important Review skippedAuto reviews are disabled on base/target branches other than the default branch. Please check the settings in the CodeRabbit UI or the ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Pro Run ID: You can disable this status message by setting the Use the checkbox below for a quick retry:
✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
1 participant
Summary
Cross-checked every documented command/option in
docs/pgatk-cli.mdagainst the actual@click.optiondecorators inpgatk/commands/*.py. Fixed only confirmed inaccuracies; subjective wording / changelog updates were left for separate PRs.Per-command fixes
generate-decoy— help block listed mostly invented short flags (-i -o -l -n -x -w -t -b -m) and two options that don't exist (--cleavage_sites,--anti_cleavage_sites). Rewrote againstproteindb_decoy.py:14-44.ensembl-downloader—-l/--list_taxonomiesdoesn't exist (likely confused withcbioportal-downloader -l/--list_studies); removed the option and the example that used it. Added the real-en/--ensembl_name,--grch37,--url_file, and-fp/--folder_prefix_releaseoptions.cosmic-downloader— added missing-P/--productsand--url_file.cbioportal-downloader— added missing-th/--multithreadingand--url_file.ncbi-downloader— added missing--grch37,--generate-transcripts,--generate-cds.vcf-to-proteindb:-c/--config_fileis notrequired=Truein the click decorator — moved to Optional.--exclude_consequencesdefault was missingregulatory_region_variant(the value inensembl_config.yamlis six terms, not five).--transcript_index/--consequence_index. Those options don't exist; the real names are--transcript_str/--consequence_str/--biotype_str.-w/--workersdefault listed as 1; actual default iscpu_count().dnaseq-to-proteindb—-c/--config_fileis optional;--num_orfsdefault is 3 (matches click help string andensembl_config.yaml), was listed as 0.cosmic-to-proteindbcell-line example —--filter_column 'Sample name'is the COSMIC v2 column name; v103 columns are uppercase (SAMPLE_NAME).#downloading-ncbi--clinvar-data(double dash) was broken because mkdocs slugify collapses/to nothing, producingdownloading-ncbi-clinvar-data(single dash).Test plan
mkdocs build --strict— zero warnings from user-facing pages (only pre-existingdocs/plans/warnings remain, all about cross-file links from the plans/ directory that are unrelated to this PR).