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Merge pull request #6 from nf-core/dev
DEV -> MASTER Release PR for initial release
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# Dockstore config version, not pipeline version | ||
version: 1.2 | ||
workflows: | ||
- subclass: nfl | ||
primaryDescriptorPath: /nextflow.config |
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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 #dualrnaseq channel" | ||
url: https://nfcore.slack.com/channels/dualrnaseq | ||
about: Discussion about the nf-core/dualrnaseq pipeline |
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--- | ||
name: Feature request | ||
about: Suggest an idea for the nf-core/dualrnaseq pipeline | ||
labels: enhancement | ||
--- | ||
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<!-- | ||
# nf-core/dualrnaseq 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/dualrnaseq pull request | ||
Many thanks for contributing to nf-core/dualrnaseq! | ||
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/dualrnaseq/tree/master/.github/CONTRIBUTING.md) | ||
--> | ||
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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/dualrnaseq branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/dualrnaseq) | ||
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). | ||
- [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py` | ||
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/dualrnaseq/tree/master/.github/CONTRIBUTING.md) | ||
- [ ] If necessary, also make a PR on the nf-core/dualrnaseq _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/dualrnaseq/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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# Markdownlint configuration file | ||
default: true, | ||
default: true | ||
line-length: false | ||
no-duplicate-header: | ||
siblings_only: true | ||
no-inline-html: | ||
allowed_elements: | ||
- img | ||
- p | ||
- kbd | ||
- details | ||
- summary |
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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: | ||
workflow_run: | ||
workflows: ["nf-core Docker push (release)"] | ||
types: [completed] | ||
workflow_dispatch: | ||
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jobs: | ||
run-awstest: | ||
name: Run AWS full tests | ||
if: github.repository == 'nf-core/dualrnaseq' | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Setup Miniconda | ||
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 | ||
# 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-dualrnaseq \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition $AWS_JOB_DEFINITION \ | ||
--container-overrides '{"command": ["nf-core/dualrnaseq", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/dualrnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/dualrnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' |
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name: nf-core AWS test | ||
# This workflow is triggered on push to the master branch. | ||
# It can be additionally triggered manually with GitHub actions workflow dispatch. | ||
# It runs the -profile 'test' on AWS batch. | ||
|
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on: | ||
workflow_dispatch: | ||
|
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jobs: | ||
run-awstest: | ||
name: Run AWS tests | ||
if: github.repository == 'nf-core/dualrnaseq' | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Setup Miniconda | ||
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 | ||
# TODO nf-core: You can customise CI pipeline run tests as required | ||
# For example: adding multiple test runs with different parameters | ||
# Remember that you can parallelise this by using strategy.matrix | ||
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-dualrnaseq \ | ||
--job-queue $AWS_JOB_QUEUE \ | ||
--job-definition $AWS_JOB_DEFINITION \ | ||
--container-overrides '{"command": ["nf-core/dualrnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/dualrnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/dualrnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' |
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