nextstrain/pathogen-repo-guide issues and pull requests

#80 - Ingest: Derive URL column during ingest

Pull Request - State: closed - Opened by j23414 about 2 months ago - 1 comment

#80 - Ingest: Derive URL column during ingest

Pull Request - State: closed - Opened by j23414 about 2 months ago - 1 comment

#79 - Standardized composable configs

Issue - State: open - Opened by joverlee521 about 2 months ago - 3 comments

#79 - Standardized composable configs

Issue - State: open - Opened by joverlee521 about 2 months ago - 3 comments

#78 - phylogenetic/nextclade: Add links to tutorials and zika/mpox repos

Pull Request - State: closed - Opened by joverlee521 2 months ago

#78 - phylogenetic/nextclade: Add links to tutorials and zika/mpox repos

Pull Request - State: closed - Opened by joverlee521 2 months ago

#77 - ingest: properly handle TSVs with `csvtk`

Pull Request - State: closed - Opened by joverlee521 2 months ago

#77 - ingest: properly handle TSVs with `csvtk`

Pull Request - State: closed - Opened by joverlee521 2 months ago

#76 - ingest: add rule to create `url` column for accessions

Issue - State: closed - Opened by joverlee521 2 months ago - 8 comments
Labels: enhancement

#76 - ingest: add rule to create `url` column for accessions

Issue - State: closed - Opened by joverlee521 2 months ago - 8 comments
Labels: enhancement

#75 - phylogenetic: Link to zika and mpox as example workflows

Issue - State: closed - Opened by joverlee521 2 months ago
Labels: documentation

#75 - phylogenetic: Link to zika and mpox as example workflows

Issue - State: closed - Opened by joverlee521 2 months ago
Labels: documentation

#74 - work needed to allow users to run analyses separate to pathogen workflows

Issue - State: open - Opened by jameshadfield 2 months ago - 4 comments
Labels: proposal

#74 - work needed to allow users to run analyses separate to pathogen workflows

Issue - State: open - Opened by jameshadfield 2 months ago - 4 comments
Labels: proposal

#73 - ingest: Switch to `full_authors` and `authors` fields

Pull Request - State: closed - Opened by joverlee521 3 months ago

#73 - ingest: Switch to `full_authors` and `authors` fields

Pull Request - State: closed - Opened by joverlee521 3 months ago

#72 - Provide a generic pattern for including additional user data alongside curated data

Issue - State: open - Opened by genehack 3 months ago - 2 comments
Labels: enhancement

#71 - ingest: Add example build-config/ci/config.yaml

Issue - State: closed - Opened by genehack 3 months ago - 1 comment

#71 - ingest: Add example build-config/ci/config.yaml

Issue - State: closed - Opened by genehack 3 months ago - 1 comment

#70 - Update nextclade workflow docs for v3

Pull Request - State: closed - Opened by joverlee521 4 months ago - 1 comment

#70 - Update nextclade workflow docs for v3

Pull Request - State: closed - Opened by joverlee521 4 months ago - 1 comment

#69 - Migrate to Nextclade v3

Issue - State: closed - Opened by joverlee521 4 months ago
Labels: enhancement

#69 - Migrate to Nextclade v3

Issue - State: closed - Opened by joverlee521 4 months ago
Labels: enhancement

#68 - Adds a recommended `is_lab_host` column to the ingested metadata.tsv file

Pull Request - State: closed - Opened by j23414 4 months ago

#68 - Adds a recommended `is_lab_host` column to the ingested metadata.tsv file

Pull Request - State: closed - Opened by j23414 4 months ago

#67 - ingest: Nextclade merge updates

Pull Request - State: closed - Opened by tsibley 4 months ago

#67 - ingest: Nextclade merge updates

Pull Request - State: closed - Opened by tsibley 4 months ago

#66 - ingest: Properly handle CSV-like TSVs

Issue - State: closed - Opened by joverlee521 4 months ago

#66 - ingest: Properly handle CSV-like TSVs

Issue - State: closed - Opened by joverlee521 4 months ago

#65 - ingest: Updates for `augur curate` and `augur merge`

Issue - State: closed - Opened by joverlee521 4 months ago - 1 comment

#64 - Bacterial workflow support

Issue - State: open - Opened by genehack 4 months ago
Labels: enhancement

#64 - Bacterial workflow support

Issue - State: open - Opened by genehack 4 months ago
Labels: enhancement

#63 - ingest: Add standardized steps for curating host

Issue - State: open - Opened by joverlee521 6 months ago
Labels: enhancement

#63 - ingest: Add standardized steps for curating host

Issue - State: open - Opened by joverlee521 6 months ago
Labels: enhancement

#62 - Link to Nextstrain docs

Pull Request - State: closed - Opened by joverlee521 6 months ago

#62 - Link to Nextstrain docs

Pull Request - State: closed - Opened by joverlee521 6 months ago

#61 - Adding ingest guide to documentation

Issue - State: closed - Opened by miparedes 6 months ago - 1 comment
Labels: documentation

#60 - ingest: Add lab host fields from NCBI Datasets

Issue - State: closed - Opened by joverlee521 6 months ago - 1 comment
Labels: enhancement

#60 - ingest: Add lab host fields from NCBI Datasets

Issue - State: closed - Opened by joverlee521 6 months ago - 1 comment
Labels: enhancement

#59 - ingest: How to handle segmented viruses

Issue - State: open - Opened by joverlee521 7 months ago - 12 comments

#59 - ingest: How to handle segmented viruses

Issue - State: open - Opened by joverlee521 7 months ago - 12 comments

#58 - Missing comma in `fetch_ncbi_dataset_package` rule causing syntax error

Issue - State: closed - Opened by BryanTegomoh 7 months ago - 5 comments
Labels: bug

#58 - Missing comma in `fetch_ncbi_dataset_package` rule causing syntax error

Issue - State: closed - Opened by BryanTegomoh 7 months ago - 5 comments
Labels: bug

#57 - ingest: Update default config params for strain

Issue - State: open - Opened by joverlee521 7 months ago - 3 comments

#57 - ingest: Update default config params for strain

Issue - State: open - Opened by joverlee521 7 months ago - 3 comments

#56 - ingest: Add build-configs for CI

Issue - State: open - Opened by joverlee521 7 months ago - 8 comments
Labels: enhancement

#56 - ingest: Add build-configs for CI

Issue - State: open - Opened by joverlee521 7 months ago - 8 comments
Labels: enhancement

#55 - ingest/nextclade: Replace `csvtk`

Issue - State: closed - Opened by joverlee521 7 months ago - 2 comments

#55 - ingest/nextclade: Replace `csvtk`

Issue - State: closed - Opened by joverlee521 7 months ago - 2 comments

#54 - Ingest nextclade updates

Pull Request - State: closed - Opened by joverlee521 7 months ago - 2 comments

#54 - Ingest nextclade updates

Pull Request - State: closed - Opened by joverlee521 7 months ago - 2 comments

#53 - ingest: use new augur curate commands

Pull Request - State: closed - Opened by joverlee521 7 months ago - 2 comments

#52 - Fix typo in `ingest/rules/curate.smk`

Pull Request - State: closed - Opened by kimandrews 7 months ago

#52 - Fix typo in `ingest/rules/curate.smk`

Pull Request - State: closed - Opened by kimandrews 7 months ago

#51 - ingest: Use of `data` vs `results` directories

Issue - State: closed - Opened by joverlee521 7 months ago - 5 comments

#51 - ingest: Use of `data` vs `results` directories

Issue - State: closed - Opened by joverlee521 7 months ago - 5 comments

#50 - ingest: Standardize steps for adding gene coverage to metadata

Issue - State: open - Opened by joverlee521 7 months ago - 4 comments
Labels: enhancement

#50 - ingest: Standardize steps for adding gene coverage to metadata

Issue - State: open - Opened by joverlee521 7 months ago - 4 comments
Labels: enhancement

#49 - ingest: use new augur curate commands

Issue - State: closed - Opened by joverlee521 7 months ago

#49 - ingest: use new augur curate commands

Issue - State: closed - Opened by joverlee521 7 months ago

#48 - Add template for phylogenetic `description.md`

Issue - State: open - Opened by joverlee521 7 months ago - 1 comment
Labels: enhancement

#48 - Add template for phylogenetic `description.md`

Issue - State: open - Opened by joverlee521 7 months ago - 1 comment
Labels: enhancement

#47 - Updates to use of Nextclade in ingest workflow

Issue - State: closed - Opened by joverlee521 8 months ago

#47 - Updates to use of Nextclade in ingest workflow

Issue - State: closed - Opened by joverlee521 8 months ago

#46 - Propagate `.gitattributes` to Nextstrain pathogen repos

Issue - State: closed - Opened by joverlee521 8 months ago - 5 comments
Labels: source: office hours

#46 - Propagate `.gitattributes` to Nextstrain pathogen repos

Issue - State: closed - Opened by joverlee521 8 months ago - 5 comments
Labels: source: office hours

#45 - Add docs for internal Nextstrain team

Pull Request - State: closed - Opened by joverlee521 8 months ago

#44 - Update `pathogen-repo-ci` to "generic"/"smart" workflow

Issue - State: closed - Opened by genehack 8 months ago - 1 comment
Labels: enhancement

#43 - Add pre-commit-config and GHA [#42]

Pull Request - State: closed - Opened by genehack 8 months ago

#43 - Add pre-commit-config and GHA [#42]

Pull Request - State: closed - Opened by genehack 8 months ago

#42 - Add pre-commit-config.yaml, pre-commit GHA, and cleanup existing files

Issue - State: closed - Opened by genehack 8 months ago - 1 comment
Labels: enhancement

#42 - Add pre-commit-config.yaml, pre-commit GHA, and cleanup existing files

Issue - State: closed - Opened by genehack 8 months ago - 1 comment
Labels: enhancement

#41 - Misc tpyoes

Pull Request - State: closed - Opened by genehack 9 months ago - 3 comments

#41 - Misc tpyoes

Pull Request - State: closed - Opened by genehack 9 months ago - 3 comments

#40 - ingest: Create new accession field without version

Pull Request - State: closed - Opened by joverlee521 10 months ago - 2 comments