Ecosyste.ms: Issues

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GitHub / nextstrain/pathogen-repo-guide issues and pull requests

#24 - profiles: rename defaults.yaml to profiles_config.yaml

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 7 comments

#24 - profiles: rename defaults.yaml to profiles_config.yaml

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 7 comments

#22 - handle bare quotes in fields

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

#21 - Add standard CI jobs for ingest workflow

Issue - State: closed - Opened by joverlee521 about 1 year ago - 2 comments

#20 - Standardize output metadata fields for Nextstrain ingest

Issue - State: open - Opened by joverlee521 about 1 year ago - 3 comments

#20 - Standardize output metadata fields for Nextstrain ingest

Issue - State: open - Opened by joverlee521 about 1 year ago - 3 comments

#19 - ingest: simplify NCBI Datasets fields config

Pull Request - State: closed - Opened by joverlee521 about 1 year ago

#19 - ingest: simplify NCBI Datasets fields config

Pull Request - State: closed - Opened by joverlee521 about 1 year ago

#18 - Add standard logging of config values

Issue - State: open - Opened by joverlee521 about 1 year ago - 8 comments
Labels: enhancement

#18 - Add standard logging of config values

Issue - State: open - Opened by joverlee521 about 1 year ago - 8 comments
Labels: enhancement

#17 - Rename repo to better reflect usage and intentions

Issue - State: closed - Opened by joverlee521 about 1 year ago - 14 comments

#17 - Rename repo to better reflect usage and intentions

Issue - State: closed - Opened by joverlee521 about 1 year ago - 14 comments

#16 - workflows: Add hardcoded `workdir` directives

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 12 comments

#15 - Additional docs

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 1 comment

#15 - Additional docs

Pull Request - State: closed - Opened by joverlee521 about 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 over 1 year ago

#13 - Update ingest vendored

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#13 - Update ingest vendored

Pull Request - State: closed - Opened by joverlee521 over 1 year ago

#12 - Reconsider including `vendored` scripts in ingest template

Issue - State: open - Opened by joverlee521 over 1 year ago - 2 comments

#12 - Reconsider including `vendored` scripts in ingest template

Issue - State: open - Opened by joverlee521 over 1 year ago - 2 comments

#11 - Ingest: Support bacterial genomes

Issue - State: open - Opened by joverlee521 over 1 year ago
Labels: enhancement

#10 - Add Nextstrain automation docs

Issue - State: closed - Opened by joverlee521 over 1 year ago - 1 comment
Labels: enhancement

#9 - Add "Getting Started" docs

Issue - State: closed - Opened by joverlee521 over 1 year ago - 1 comment
Labels: enhancement

#8 - Add optional BioSample rules to ingest pipeline

Issue - State: open - Opened by joverlee521 over 1 year ago
Labels: enhancement

#7 - Add Nextclade to ingest

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#6 - Ingest curate fixes

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 1 comment

#5 - Remove `nextclade_datasets` directory and references

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 3 comments

#4 - Put default values in ingest config, or suggest options in comments

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 4 comments
Labels: enhancement

#3 - Run snakefmt on snakefiles

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago

#2 - fix minor typos

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago - 1 comment

#1 - fixes

Pull Request - State: closed - Opened by corneliusroemer over 1 year ago