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name: nf-core AWS full size tests
# This workflow is triggered on push to the master branch.
# It runs the -profile 'test_full' on AWS batch
on:
release:
types: [published]
jobs:
run-awstest:
name: Run AWS full tests
if: github.repository == 'nf-core/hic'
runs-on: ubuntu-latest
steps:
- name: Setup Miniconda
uses: goanpeca/setup-miniconda@v1.0.2
with:
auto-update-conda: true
python-version: 3.7
- name: Install awscli
run: conda install -c conda-forge awscli
- name: Start AWS batch job
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
# Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
run: |
aws batch submit-job \
--region eu-west-1 \
--job-name nf-core-hic \
--job-queue $AWS_JOB_QUEUE \
--job-definition $AWS_JOB_DEFINITION \
--container-overrides '{"command": ["nf-core/hic", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/hic/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/hic/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'