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Merge pull request #545 from nf-core/dev
Version 1.9 release
2 parents 9e33e7f + c461d55 commit 397b886

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‎.github/.coveragerc

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[run]
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omit = nf_core/pipeline-template/*

‎.github/CONTRIBUTING.md

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@@ -38,7 +38,7 @@ The HTML will then be generated in `docs/api/_build/html`.
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## Tests
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When you create a pull request with changes, [Travis CI](https://travis-ci.com/) will run automatic tests.
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When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
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Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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There are two types of tests that run:
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```
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### Lint Tests
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The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
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nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
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To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
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The nf-core/tools repo itself contains the master template for creating new nf-core pipelines.
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Travis is set up to create a new pipeline from this template and then run the lint tests on it.
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Once you have created a new pipeline from this template GitHub Actions is automatically set up to run lint tests on it.
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This ensures that any changes we make to either the linting or the template stay in sync.
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You can replicate this process locally with the following commands:
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‎.github/RELEASE_CHECKLIST.md

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## Before release
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1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
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2. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
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3. Make sure all CI tests are passing!
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4. Create a PR from `dev` to `master`
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5. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
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6. Request review (2 approvals required)
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7. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where *Prefix* = *Metal* and *Dictionary* = *Animal*.
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8. Merge the PR into `master`
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9. Once CI tests on commit have passed, create a new release copying the `CHANGELOG` for that release into the description section.
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## After release
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1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
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2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
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3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
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4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`

‎.github/coveragerc

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‎.github/workflows/code-tests.yml

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name: Python tests
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# This workflow is triggered on pushes and PRs to the repository.
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on: [push, pull_request]
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jobs:
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PythonLint:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.6, 3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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name: Check out source-code repository
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip pytest pytest-datafiles pytest-cov mock jsonschema
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pip install .
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- name: Install Nextflow
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run: |
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mkdir /tmp/nextflow
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cd /tmp/nextflow
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wget -qO- get.nextflow.io | bash
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sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
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- name: Lint with flake8
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run: |
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: python3 -m pytest --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
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- uses: codecov/codecov-action@v1
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name: Upload code coverage report
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with:
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if: success()
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/create-lint-wf.yml

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name: Create a pipeline and lint it
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on: [push, pull_request]
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jobs:
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MakeTestWorkflow:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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name: Check out source-code repository
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .
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- name: Install Nextflow
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run: |
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mkdir /tmp/nextflow
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cd /tmp/nextflow
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wget -qO- get.nextflow.io | bash
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sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
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- name: Run nf-core tools
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run: |
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nf-core create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
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nf-core lint nf-core-testpipeline

‎.github/workflows/deploy-pypi.yml

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name: Publish nf-core to PyPI
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on:
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release:
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types: [published]
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jobs:
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build-n-publish:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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name: Check out source-code repository
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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pip install .
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- name: Build the distribution
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run: python setup.py sdist bdist_wheel
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- name: Publish dist to PyPI
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if: github.repository == 'nf-core/tools'
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uses: pypa/gh-action-pypi-publish@master
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with:
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password: ${{ secrets.pypi_password }}

‎.github/workflows/markdown-lint.yml

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name: Lint Markdown
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on: [push, pull_request]
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jobs:
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Markdown:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-node@v1
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with:
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node-version: '10'
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- name: Install markdownlint
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run: npm install -g markdownlint-cli
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- name: Run Markdownlint
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run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml

‎.github/workflows/sync.yml

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name: Sync template
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on:
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release:
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types: [published]
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jobs:
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sync-all:
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name: Sync all pipelines
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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name: Check out source-code repository
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .
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- name: Run synchronisation
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if: github.repository == 'nf-core/tools'
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env:
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AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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run: nf-core sync --all --username nf-core-bot --auth-token $AUTH_TOKEN

‎.github/workflows/tools-api-docs.yml

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name: nf-core/tools API docs
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on:
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push:
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branches: [master, dev]
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jobs:
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build-n-publish:
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name: Build and publish nf-core to PyPI
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runs-on: ubuntu-18.04
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steps:
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- name: Check out source-code repository
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uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install python dependencies
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run: |
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python -m pip install --upgrade pip Sphinx sphinxcontrib-napoleon
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pip install .
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- name: Build HTML docs
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run: make --directory ./docs/api html
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- name: Push docs to api-doc branch
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if: github.repository == 'nf-core/tools'
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run: |
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git checkout --orphan api-doc
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git rm -r --cache .
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git config user.email "[email protected]"
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git config user.name "nf-core-bot"
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git add docs
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git commit --message "nf-core/tools docs build
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$GITHUB_REF - $GITHUB_SHA
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"
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git remote add nf-core https://github.com/nf-core/tools.git
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git push --force --set-upstream nf-core api-doc

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