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Merge pull request #185 from nf-core/dev
Dev -> Master for v2.0 release
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root = true | ||
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[*] | ||
charset = utf-8 | ||
end_of_line = lf | ||
insert_final_newline = true | ||
trim_trailing_whitespace = true | ||
indent_size = 4 | ||
indent_style = space | ||
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[*.{yml,yaml}] | ||
indent_size = 2 | ||
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# These files are edited and tested upstream in nf-core/modules | ||
[/modules/nf-core/**] | ||
charset = unset | ||
end_of_line = unset | ||
insert_final_newline = unset | ||
trim_trailing_whitespace = unset | ||
indent_style = unset | ||
indent_size = unset | ||
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[/assets/email*] | ||
indent_size = unset |
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# Dockstore config version, not pipeline version | ||
version: 1.2 | ||
workflows: | ||
- subclass: nfl | ||
primaryDescriptorPath: /nextflow.config | ||
publish: True |
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blank_issues_enabled: false | ||
contact_links: | ||
- name: Join nf-core | ||
url: https://nf-co.re/join | ||
about: Please join the nf-core community here | ||
- name: "Slack #viralrecon channel" | ||
url: https://nfcore.slack.com/channels/viralrecon | ||
about: Discussion about the nf-core/viralrecon pipeline |
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--- | ||
name: Feature request | ||
about: Suggest an idea for the nf-core/viralrecon pipeline | ||
labels: enhancement | ||
--- | ||
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<!-- | ||
# nf-core/viralrecon feature request | ||
Hi there! | ||
Thanks for suggesting a new feature for the pipeline! | ||
Please delete this text and anything that's not relevant from the template below: | ||
--> | ||
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## Is your feature request related to a problem? Please describe | ||
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A clear and concise description of what the problem is. | ||
<!-- A clear and concise description of what the problem is. --> | ||
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Ex. I'm always frustrated when [...] | ||
<!-- e.g. [I'm always frustrated when ...] --> | ||
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## Describe the solution you'd like | ||
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A clear and concise description of what you want to happen. | ||
<!-- A clear and concise description of what you want to happen. --> | ||
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## Describe alternatives you've considered | ||
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A clear and concise description of any alternative solutions or features you've considered. | ||
<!-- A clear and concise description of any alternative solutions or features you've considered. --> | ||
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## Additional context | ||
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Add any other context about the feature request here. | ||
<!-- Add any other context about the feature request here. --> |
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<!-- | ||
# nf-core/viralrecon pull request | ||
Many thanks for contributing to nf-core/viralrecon! | ||
Please fill in the appropriate checklist below (delete whatever is not relevant). | ||
These are the most common things requested on pull requests (PRs). | ||
Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. | ||
Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md) | ||
--> | ||
<!-- markdownlint-disable ul-indent --> | ||
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## PR checklist | ||
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- [ ] This comment contains a description of changes (with reason) | ||
- [ ] This comment contains a description of changes (with reason). | ||
- [ ] If you've fixed a bug or added code that should be tested, add tests! | ||
- [ ] If necessary, also make a PR on the [nf-core/viralrecon branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/viralrecon) | ||
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). | ||
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md) | ||
- [ ] If necessary, also make a PR on the nf-core/viralrecon _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. | ||
- [ ] Make sure your code lints (`nf-core lint .`). | ||
- [ ] Documentation in `docs` is updated | ||
- [ ] `CHANGELOG.md` is updated | ||
- [ ] `README.md` is updated | ||
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**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md) | ||
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). | ||
- [ ] Usage Documentation in `docs/usage.md` is updated. | ||
- [ ] Output Documentation in `docs/output.md` is updated. | ||
- [ ] `CHANGELOG.md` is updated. | ||
- [ ] `README.md` is updated (including new tool citations and authors/contributors). |
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name: nf-core AWS full test | ||
# This workflow is triggered on releases. | ||
name: nf-core AWS full size tests | ||
# This workflow is triggered on published releases. | ||
# It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
# It runs the -profile 'test_full' on AWS batch | ||
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on: | ||
release: | ||
types: [published] | ||
workflow_dispatch: | ||
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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 }} | ||
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jobs: | ||
run-awstest: | ||
name: Run AWS full tests | ||
if: github.repository == 'nf-core/viralrecon' | ||
name: Run AWS test | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
platform: ['illumina', 'nanopore'] | ||
steps: | ||
- name: Setup Miniconda | ||
uses: goanpeca/setup-miniconda@v1.0.2 | ||
uses: conda-incubator/setup-miniconda@v2 | ||
with: | ||
auto-update-conda: true | ||
python-version: 3.7 | ||
- name: Install awscli | ||
run: conda install -c conda-forge awscli | ||
- name: Start AWS batch job | ||
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: | # Submits job to AWS batch using a 'nextflow-4GiB' job definition. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files. | ||
# Do a full-scale run with data from each sequencing platform | ||
run: | | ||
aws batch submit-job \ | ||
--region eu-west-1 \ | ||
--job-name nf-core-viralrecon \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition nextflow-4GiB \ | ||
--container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}' | ||
--region eu-west-1 \ | ||
--job-name nf-core-viralrecon \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition $AWS_JOB_DEFINITION \ | ||
--container-overrides '{"command": ["nf-core/viralrecon", "-r '"${GITHUB_SHA}"' -profile test_full_'"${{matrix.platform}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/viralrecon/results-'"${GITHUB_SHA}"'/platform_'"${{matrix.platform}}"' -w s3://'"${AWS_S3_BUCKET}"'/viralrecon/work-'"${GITHUB_SHA}"'/'"${{matrix.platform}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' |
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