GitHub / nextstrain/pathogen-repo-guide issues and pull requests
#80 - Ingest: Derive URL column during ingest
Pull Request -
State: closed - Opened by j23414 8 months ago
- 1 comment
#79 - Standardized composable configs
Issue -
State: open - Opened by joverlee521 8 months ago
- 3 comments
#78 - phylogenetic/nextclade: Add links to tutorials and zika/mpox repos
Pull Request -
State: closed - Opened by joverlee521 8 months ago
#77 - ingest: properly handle TSVs with `csvtk`
Pull Request -
State: closed - Opened by joverlee521 8 months ago
#76 - ingest: add rule to create `url` column for accessions
Issue -
State: closed - Opened by joverlee521 8 months ago
- 8 comments
Labels: enhancement
#75 - phylogenetic: Link to zika and mpox as example workflows
Issue -
State: closed - Opened by joverlee521 8 months ago
Labels: documentation
#74 - work needed to allow users to run analyses separate to pathogen workflows
Issue -
State: open - Opened by jameshadfield 8 months ago
- 4 comments
Labels: proposal
#73 - ingest: Switch to `full_authors` and `authors` fields
Pull Request -
State: closed - Opened by joverlee521 8 months ago
#72 - Provide a generic pattern for including additional user data alongside curated data
Issue -
State: open - Opened by genehack 9 months ago
- 2 comments
Labels: enhancement
#71 - ingest: Add example build-config/ci/config.yaml
Issue -
State: closed - Opened by genehack 9 months ago
- 1 comment
#70 - Update nextclade workflow docs for v3
Pull Request -
State: closed - Opened by joverlee521 9 months ago
- 1 comment
#69 - Migrate to Nextclade v3
Issue -
State: closed - Opened by joverlee521 10 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 10 months ago
#67 - ingest: Nextclade merge updates
Pull Request -
State: closed - Opened by tsibley 10 months ago
#66 - ingest: Properly handle CSV-like TSVs
Issue -
State: closed - Opened by joverlee521 10 months ago
#65 - ingest: Updates for `augur curate` and `augur merge`
Issue -
State: closed - Opened by joverlee521 10 months ago
- 1 comment
#64 - Bacterial workflow support
Issue -
State: open - Opened by genehack 10 months ago
Labels: enhancement
#63 - ingest: Add standardized steps for curating host
Issue -
State: open - Opened by joverlee521 11 months ago
Labels: enhancement
#62 - Link to Nextstrain docs
Pull Request -
State: closed - Opened by joverlee521 12 months ago
#61 - Adding ingest guide to documentation
Issue -
State: closed - Opened by miparedes 12 months ago
- 1 comment
Labels: documentation
#60 - ingest: Add lab host fields from NCBI Datasets
Issue -
State: closed - Opened by joverlee521 12 months ago
- 1 comment
Labels: enhancement
#59 - ingest: How to handle segmented viruses
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 12 comments
#58 - Missing comma in `fetch_ncbi_dataset_package` rule causing syntax error
Issue -
State: closed - Opened by BryanTegomoh about 1 year ago
- 5 comments
Labels: bug
#57 - ingest: Update default config params for strain
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 3 comments
#56 - ingest: Add build-configs for CI
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 8 comments
Labels: enhancement
#55 - ingest/nextclade: Replace `csvtk`
Issue -
State: closed - Opened by joverlee521 about 1 year ago
- 2 comments
#54 - Ingest nextclade updates
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
- 2 comments
#53 - ingest: use new augur curate commands
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
- 2 comments
#52 - Fix typo in `ingest/rules/curate.smk`
Pull Request -
State: closed - Opened by kimandrews about 1 year ago
#51 - ingest: Use of `data` vs `results` directories
Issue -
State: closed - Opened by joverlee521 about 1 year ago
- 5 comments
#50 - ingest: Standardize steps for adding gene coverage to metadata
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 4 comments
Labels: enhancement
#49 - ingest: use new augur curate commands
Issue -
State: closed - Opened by joverlee521 about 1 year ago
#48 - Add template for phylogenetic `description.md`
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 1 comment
Labels: enhancement
#47 - Updates to use of Nextclade in ingest workflow
Issue -
State: closed - Opened by joverlee521 about 1 year ago
#46 - Propagate `.gitattributes` to Nextstrain pathogen repos
Issue -
State: closed - Opened by joverlee521 about 1 year ago
- 5 comments
Labels: source: office hours
#45 - Add docs for internal Nextstrain team
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
#44 - Update `pathogen-repo-ci` to "generic"/"smart" workflow
Issue -
State: closed - Opened by genehack about 1 year ago
- 1 comment
Labels: enhancement
#43 - Add pre-commit-config and GHA [#42]
Pull Request -
State: closed - Opened by genehack about 1 year ago
#42 - Add pre-commit-config.yaml, pre-commit GHA, and cleanup existing files
Issue -
State: closed - Opened by genehack about 1 year ago
- 1 comment
Labels: enhancement
#41 - Misc tpyoes
Pull Request -
State: closed - Opened by genehack about 1 year ago
- 3 comments
#40 - ingest: Create new accession field without version
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 2 comments
#39 - ingest: GenBank accession should not include version number
Issue -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
Labels: enhancement
#38 - ingest: Provide target for raw metadata from NCBI Datasets
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
#37 - Add .gitattibutes to force line endings to be LF
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
#36 - ingest/build-configs/nextstrain-automation: Add README
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
#35 - ingest/nextstrain-automation: Fix upload_to_s3
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
#34 - ingest: Move Nextclade configs to separate YAML
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
#33 - ingest: Add default values to config.yaml
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 2 comments
#32 - ingest: Move intermediate files to `data` directory
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
#31 - Update ingest to output to data/ for intermediate files
Issue -
State: closed - Opened by joverlee521 over 1 year ago
#30 - Provide a no-curation option for NCBI Ingest
Issue -
State: closed - Opened by j23414 over 1 year ago
- 1 comment
Labels: enhancement
#29 - Add top level nextstrain-pathogen.yaml file
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
#28 - Pathogen repo linter
Issue -
State: open - Opened by joverlee521 over 1 year ago
#27 - Rename "profiles" to "build-configs"
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 10 comments
#26 - How should we standardize config schema for files?
Issue -
State: open - Opened by joverlee521 over 1 year ago
- 3 comments
#25 - How should we standardize GitHub Action workflows per repo?
Issue -
State: open - Opened by joverlee521 over 1 year ago
- 8 comments
#24 - profiles: rename defaults.yaml to profiles_config.yaml
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 7 comments
#23 - Version nextclade binary for transition, i.e. nextclade -> nextclade2
Pull Request -
State: closed - Opened by corneliusroemer over 1 year ago
#22 - handle bare quotes in fields
Pull Request -
State: closed - Opened by j23414 over 1 year ago
- 1 comment
#21 - Add standard CI jobs for ingest workflow
Issue -
State: closed - Opened by joverlee521 over 1 year ago
- 2 comments
#20 - Standardize output metadata fields for Nextstrain ingest
Issue -
State: open - Opened by joverlee521 over 1 year ago
- 3 comments
#19 - ingest: simplify NCBI Datasets fields config
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
#18 - Add standard logging of config values
Issue -
State: open - Opened by joverlee521 over 1 year ago
- 8 comments
Labels: enhancement
#17 - Rename repo to better reflect usage and intentions
Issue -
State: closed - Opened by joverlee521 over 1 year ago
- 14 comments
#16 - workflows: Add hardcoded `workdir` directives
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 12 comments
#15 - Additional docs
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
- 1 comment
#14 - fix: dropping the first line in a bare nextclade_field_map.tsv
Pull Request -
State: closed - Opened by j23414 almost 2 years ago
#13 - Update ingest vendored
Pull Request -
State: closed - Opened by joverlee521 almost 2 years ago
#12 - Reconsider including `vendored` scripts in ingest template
Issue -
State: open - Opened by joverlee521 almost 2 years ago
- 2 comments
#11 - Ingest: Support bacterial genomes
Issue -
State: open - Opened by joverlee521 almost 2 years ago
Labels: enhancement
#10 - Add Nextstrain automation docs
Issue -
State: closed - Opened by joverlee521 almost 2 years ago
- 1 comment
Labels: enhancement
#9 - Add "Getting Started" docs
Issue -
State: closed - Opened by joverlee521 almost 2 years ago
- 1 comment
Labels: enhancement
#8 - Add optional BioSample rules to ingest pipeline
Issue -
State: open - Opened by joverlee521 almost 2 years ago
Labels: enhancement
#7 - Add Nextclade to ingest
Pull Request -
State: closed - Opened by joverlee521 almost 2 years ago
- 1 comment
#6 - Ingest curate fixes
Pull Request -
State: closed - Opened by joverlee521 almost 2 years ago
- 1 comment
#5 - Remove `nextclade_datasets` directory and references
Pull Request -
State: closed - Opened by joverlee521 almost 2 years ago
- 3 comments
#4 - Put default values in ingest config, or suggest options in comments
Issue -
State: closed - Opened by corneliusroemer almost 2 years ago
- 4 comments
Labels: enhancement
#3 - Run snakefmt on snakefiles
Pull Request -
State: closed - Opened by corneliusroemer almost 2 years ago
#2 - fix minor typos
Pull Request -
State: closed - Opened by corneliusroemer almost 2 years ago
- 1 comment
#1 - fixes
Pull Request -
State: closed - Opened by corneliusroemer almost 2 years ago