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Template update for nf-core/tools version 3.1.0
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‎.github/CONTRIBUTING.md

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# nf-core/chipseq: Contributing Guidelines
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# `nf-core/chipseq`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/chipseq.
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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- On your own fork, make a new branch `patch` based on `upstream/master`.
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- A PR should be made on `master` from patch to directly this particular bug.
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Getting help
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For further information/help, please consult the [nf-core/chipseq documentation](https://nf-co.re/chipseq/usage) and don't hesitate to get in touch on the nf-core Slack [#chipseq](https://nfcore.slack.com/channels/chipseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Pipeline contribution conventions
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To make the nf-core/chipseq code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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To make the `nf-core/chipseq` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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### Adding a new step
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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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1. Define the corresponding input channel into your new process from the expected previous process channel.
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new parameters to `nextflow.config` with a default (see below).
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
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‎.github/workflows/awsfulltest.yml

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name: nf-core AWS full size tests
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# This workflow is triggered on PRs opened against the master branch.
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# This workflow is triggered on PRs opened against the main/master branch.
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# It can be additionally triggered manually with GitHub actions workflow dispatch button.
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# It runs the -profile 'test_full' on AWS batch
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on:
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pull_request:
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branches:
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- main
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- master
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workflow_dispatch:
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pull_request_review:
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if: github.repository == 'nf-core/chipseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
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runs-on: ubuntu-latest
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steps:
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- uses: octokit/[email protected]
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- name: Get PR reviews
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uses: octokit/[email protected]
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- id: test_variables
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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run: |
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
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test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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# TODO nf-core: You can customise AWS full pipeline tests as required

‎.github/workflows/branch.yml

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name: nf-core branch protection
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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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# This workflow is triggered on PRs to `main`/`master` branch on the repository
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# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
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on:
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pull_request_target:
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branches: [master]
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branches:
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- main
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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# PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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- name: Check PRs
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if: github.repository == 'nf-core/chipseq'
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run: |
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uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
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with:
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message: |
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## This PR is against the `master` branch :x:
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## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
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* Do not close this PR
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* Click _Edit_ and change the `base` to `dev`
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Hi @${{ github.event.pull_request.user.login }},
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
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The `master` branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
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The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
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Note that even after this, the test will continue to show as failing until you push a new commit.

‎.github/workflows/ci.yml

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profile: "singularity"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Set up Nextflow
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uses: nf-core/setup-nextflow@v2

‎.github/workflows/download_pipeline.yml

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# Run the workflow when:
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# - dispatched manually
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# - when a PR is opened or reopened to master branch
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# - when a PR is opened or reopened to main/master branch
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# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
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on:
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workflow_dispatch:
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- edited
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- synchronize
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branches:
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- main
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- master
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pull_request_target:
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branches:
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- main
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- master
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env:
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- name: Disk space cleanup
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.12"
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architecture: "x64"
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--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
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--compress "none" \
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--container-system 'singularity' \
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--container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
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--container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
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--container-cache-utilisation 'amend' \
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--download-configuration 'yes'
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‎.github/workflows/fix-linting.yml

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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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# Install and run pre-commit
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.12"
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‎.github/workflows/linting.yml

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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Set up Python 3.12
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uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.12"
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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architecture: "x64"
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
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uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
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with:
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name: linting-logs
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path: |

‎.github/workflows/linting_comment.yml

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runs-on: ubuntu-latest
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steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
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uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
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with:
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workflow: linting.yml
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.10"
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- name: Install dependencies

‎.github/workflows/template_version_comment.yml

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steps:
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- name: Check out pipeline code
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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‎.gitpod.yml

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nextflow self-update
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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#- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
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- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
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- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
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- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
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- nextflow.nextflow # Nextflow syntax highlighting
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- oderwat.indent-rainbow # Highlight indentation level
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- streetsidesoftware.code-spell-checker # Spelling checker for source code
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- charliermarsh.ruff # Code linter Ruff
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extensions:
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- nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack

‎.nf-core.yml

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bump_version: null
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lint:
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nextflow_config:
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- config_defaults:
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- params.bamtools_filter_se_config
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- params.bamtools_filter_pe_config
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nf_core_version: 3.0.2
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org_path: null
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nf_core_version: 3.1.0
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repository_type: pipeline
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template:
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author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P
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name: chipseq
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org: nf-core
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outdir: .
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skip_features: null
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version: 2.2.0dev
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update: null

‎.vscode/settings.json

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{
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"markdown.styles": ["public/vscode_markdown.css"]
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}

‎conf/base.config

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maxErrors = '-1'
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// Process-specific resource requirements
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// NOTE - Please try and re-use the labels below as much as possible.
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// NOTE - Please try and reuse the labels below as much as possible.
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// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
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// If possible, it would be nice to keep the same label naming convention when
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// adding in your local modules too.

‎conf/modules.config

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withName: FASTQC {
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ext.args = '--quiet'
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}
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withName: 'MULTIQC' {
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ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
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publishDir = [

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