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workflows: create separate workflows for GenBank/GISAID ingests
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name: '[branch] Ingest 2019-nCov/SARS-CoV-2 data from GenBank for nextstrain.org/ncov' | ||
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on: | ||
push: | ||
branches-ignore: | ||
- master | ||
tags-ignore: | ||
- '**' | ||
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jobs: | ||
ingest: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v1 | ||
- name: ingest | ||
run: | | ||
PATH="$HOME/.local/bin:$PATH" | ||
python3 -m pip install --upgrade pip setuptools | ||
python3 -m pip install pipenv | ||
pipenv sync | ||
pipenv run ./bin/ingest-genbank | ||
env: | ||
AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | ||
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} |
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Original file line number | Diff line number | Diff line change |
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name: Ingest 2019-nCov/SARS-CoV-2 data from GenBank for nextstrain.org/ncov | ||
|
||
on: | ||
push: | ||
branches: | ||
- master | ||
tags-ignore: | ||
- '**' | ||
paths: | ||
- source-data/genbank_annotations.tsv | ||
|
||
schedule: | ||
# See table of scheduled times in the README. Times here are UTC. | ||
- cron: '0 6,12,15,21 * * *' | ||
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# Manually triggered using `./bin/trigger ingest` | ||
repository_dispatch: | ||
types: ingest | ||
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||
jobs: | ||
ingest: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v1 | ||
- name: ingest | ||
run: | | ||
PATH="$HOME/.local/bin:$PATH" | ||
python3 -m pip install --upgrade pip setuptools | ||
python3 -m pip install pipenv | ||
pipenv sync | ||
pipenv run ./bin/ingest-genbank | ||
env: | ||
AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | ||
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} |
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