nextstrain/zika issues and pull requests

#78 - Ingest: Derive url and use accession fields during ingest

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

#77 - Move `url` and `accession` column generation to ingest

Issue - State: open - Opened by j23414 about 2 months ago
Labels: enhancement

#76 - Use augur merge for sequences

Pull Request - State: open - Opened by victorlin 2 months ago - 2 comments
Labels: blocked

#75 - Use augur merge

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

#74 - Properly handle CSV-like TSVs

Issue - State: open - Opened by joverlee521 2 months ago

#73 - Use `augur merge` to spike in USVI records

Issue - State: closed - Opened by j23414 2 months ago - 2 comments
Labels: enhancement

#72 - Default tip label

Pull Request - State: closed - Opened by joverlee521 5 months ago - 3 comments

#72 - Default tip label

Pull Request - State: closed - Opened by joverlee521 5 months ago - 3 comments

#71 - Add .gitattributes file

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

#70 - CI: Switch CI to `pathogen-repo-ci` workflow

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

#70 - CI: Switch CI to `pathogen-repo-ci` workflow

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

#69 - ingest: use new augur curate commands

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

#68 - ingest: use new augur curate commands

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

#68 - ingest: use new augur curate commands

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

#67 - Update description

Pull Request - State: closed - Opened by j23414 7 months ago

#67 - Update description

Pull Request - State: closed - Opened by j23414 7 months ago

#66 - Use `ingest/scripts` to match `phylogenetic/scripts`

Pull Request - State: closed - Opened by j23414 7 months ago - 2 comments

#66 - Use `ingest/scripts` to match `phylogenetic/scripts`

Pull Request - State: closed - Opened by j23414 7 months ago - 2 comments

#65 - Adds data provenance attribution

Pull Request - State: closed - Opened by j23414 8 months ago

#65 - Adds data provenance attribution

Pull Request - State: closed - Opened by j23414 8 months ago

#64 - Update maintainers to Nextstrain team

Pull Request - State: closed - Opened by j23414 8 months ago

#64 - Update maintainers to Nextstrain team

Pull Request - State: closed - Opened by j23414 8 months ago

#63 - Rename phylogenetic CI config file to standard name

Pull Request - State: closed - Opened by genehack 8 months ago - 3 comments

#63 - Rename phylogenetic CI config file to standard name

Pull Request - State: closed - Opened by genehack 8 months ago - 3 comments

#62 - ENH: Add an E gene tree

Issue - State: open - Opened by j23414 8 months ago - 1 comment
Labels: enhancement

#61 - add nextstrain-pathogen.yaml [#60]

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

#61 - add nextstrain-pathogen.yaml [#60]

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

#60 - Add `nextstrain-pathogen.yaml`

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

#60 - Add `nextstrain-pathogen.yaml`

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

#59 - Switch AWS credentials from a long-lived IAM user to short-lived role sessions

Pull Request - State: closed - Opened by tsibley 8 months ago - 4 comments

#59 - Switch AWS credentials from a long-lived IAM user to short-lived role sessions

Pull Request - State: closed - Opened by tsibley 8 months ago - 4 comments

#58 - ingest: fix csvtk quotes

Pull Request - State: closed - Opened by joverlee521 9 months ago - 3 comments

#58 - ingest: fix csvtk quotes

Pull Request - State: closed - Opened by joverlee521 9 months ago - 3 comments

#57 - phylogenetic: Use inline root sequence

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

#56 - phylogenetic: Add root-sequence.json to rule `all`

Pull Request - State: closed - Opened by joverlee521 10 months ago - 3 comments

#56 - phylogenetic: Add root-sequence.json to rule `all`

Pull Request - State: closed - Opened by joverlee521 10 months ago - 3 comments

#55 - Add independent ingest and phylogenetic GH Action workflows

Pull Request - State: closed - Opened by joverlee521 10 months ago - 7 comments

#55 - Add independent ingest and phylogenetic GH Action workflows

Pull Request - State: closed - Opened by joverlee521 10 months ago - 7 comments

#54 - Fix automation hash

Pull Request - State: closed - Opened by joverlee521 10 months ago - 1 comment

#54 - Fix automation hash

Pull Request - State: closed - Opened by joverlee521 10 months ago - 1 comment

#53 - Automation cache not working as expected

Issue - State: closed - Opened by joverlee521 10 months ago - 3 comments
Labels: bug

#53 - Automation cache not working as expected

Issue - State: closed - Opened by joverlee521 10 months ago - 3 comments
Labels: bug

#52 - Automate ingest and phylogenetic workflows

Pull Request - State: closed - Opened by joverlee521 10 months ago - 3 comments

#52 - Automate ingest and phylogenetic workflows

Pull Request - State: closed - Opened by joverlee521 10 months ago - 3 comments

#51 - Add nextstrain-automation build-configs to phylogenetic worklfow

Pull Request - State: closed - Opened by joverlee521 11 months ago

#50 - Move nextstrain automation rules and configs to ingest/build-configs

Pull Request - State: closed - Opened by j23414 11 months ago - 1 comment

#50 - Move nextstrain automation rules and configs to ingest/build-configs

Pull Request - State: closed - Opened by j23414 11 months ago - 1 comment

#49 - Update maintainers

Pull Request - State: closed - Opened by trvrb 11 months ago

#49 - Update maintainers

Pull Request - State: closed - Opened by trvrb 11 months ago

#48 - Move hardcoded parameters to the config file

Pull Request - State: closed - Opened by j23414 11 months ago - 1 comment

#48 - Move hardcoded parameters to the config file

Pull Request - State: closed - Opened by j23414 11 months ago - 1 comment

#47 - Update docs to use "defaults" and "build-configs" dirs

Pull Request - State: closed - Opened by j23414 11 months ago

#47 - Update docs to use "defaults" and "build-configs" dirs

Pull Request - State: closed - Opened by j23414 11 months ago

#46 - ingest: support `custom_rules` from config

Pull Request - State: closed - Opened by joverlee521 11 months ago

#46 - ingest: support `custom_rules` from config

Pull Request - State: closed - Opened by joverlee521 11 months ago

#45 - [readme] rename config/ to default/

Issue - State: closed - Opened by jameshadfield 11 months ago

#45 - [readme] rename config/ to default/

Issue - State: closed - Opened by jameshadfield 11 months ago

#44 - Move Nextstrain "automation rules/configs" to "ingest/build-configs"

Issue - State: closed - Opened by j23414 11 months ago
Labels: enhancement

#44 - Move Nextstrain "automation rules/configs" to "ingest/build-configs"

Issue - State: closed - Opened by j23414 11 months ago
Labels: enhancement

#43 - Rename "profiles" to "build-configs"

Pull Request - State: closed - Opened by j23414 11 months ago

#43 - Rename "profiles" to "build-configs"

Pull Request - State: closed - Opened by j23414 11 months ago

#42 - ingest: Fix field_map config

Pull Request - State: closed - Opened by joverlee521 11 months ago