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Merge pull request #137 from sanger-tol/dev
Dev2Main - [1.6.0] - UNSC Trafalgar
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.github/workflows/branch.yml

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@@ -1,46 +1,24 @@
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name: nf-core branch protection
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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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name: "Close user-tagged issues and PRs"
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on:
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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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schedule:
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- cron: "0 0 * * 0" # Once a week
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jobs:
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test:
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clean-up:
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runs-on: ubuntu-latest
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permissions:
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issues: write
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pull-requests: write
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steps:
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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 == 'sanger-tol/curationpretext'
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run: |
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/curationpretext ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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# If the above check failed, post a comment on the PR explaining the failure
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
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- uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
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with:
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message: |
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## This PR is against the `${{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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* This CI test will remain failed until you push a new commit
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---
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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 }}) ${{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.
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Thanks again for your contribution!
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
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stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
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close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
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days-before-stale: 30
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days-before-close: 20
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days-before-pr-close: -1
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any-of-labels: "awaiting-changes,awaiting-feedback"
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exempt-issue-labels: "WIP"
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exempt-pr-labels: "WIP"
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repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/clean-up.yml

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issues: write
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pull-requests: write
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steps:
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- uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
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- uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
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with:
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stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
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stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

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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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
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with:
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python-version: "3.13"
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python-version: "3.14"
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architecture: "x64"
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- name: Setup Apptainer
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install git+https://github.com/nf-core/tools.git@dev
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pip install git+https://github.com/nf-core/tools.git
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- name: Make a cache directory for the container images
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run: |
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# fi
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# - name: Upload Nextflow logfile for debugging purposes
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# uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
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# uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
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# with:
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# name: nextflow_logfile.txt
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# path: .nextflow.log*

.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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# indication that the linting is being fixed
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- name: React on comment
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: eyes
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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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
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with:
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python-version: "3.13"
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python-version: "3.14"
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- name: Install pre-commit
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run: pip install pre-commit
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# indication that the linting has finished
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- name: react if linting finished succesfully
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if: steps.pre-commit.outcome == 'success'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: "+1"
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- name: react if linting errors were fixed
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id: react-if-fixed
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if: steps.commit-and-push.outcome == 'success'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: hooray
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- name: react if linting errors were not fixed
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if: steps.commit-and-push.outcome == 'failure'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: confused
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- name: react if linting errors were not fixed
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if: steps.commit-and-push.outcome == 'failure'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
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with:
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issue-number: ${{ github.event.issue.number }}
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body: |

.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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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- name: Set up Python 3.13
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uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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- name: Set up Python 3.14
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uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
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with:
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python-version: "3.13"
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python-version: "3.14"
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- name: Install pre-commit
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run: pip install pre-commit
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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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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- uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
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with:
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python-version: "3.13"
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python-version: "3.14"
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architecture: "x64"
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- name: read .nf-core.yml
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
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uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
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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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run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
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- name: Post PR comment
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uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
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uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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NFT_VER: "0.9.2"
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NFT_VER: "0.9.3"
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NFT_WORKDIR: "~"
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NXF_ANSI_LOG: false
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NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
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rm -rf ./* || true
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rm -rf ./.??* || true
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ls -la ./
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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with:
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fetch-depth: 0
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- isMain: false
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profile: "singularity"
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NXF_VER:
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- "24.10.5"
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- "25.04.0"
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- "latest-everything"
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env:
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NXF_ANSI_LOG: false
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TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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with:
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fetch-depth: 0
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continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
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env:
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NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
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NXF_VERSION: ${{ matrix.NXF_VER }}
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with:
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profile: ${{ matrix.profile }}
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shard: ${{ matrix.shard }}

.github/workflows/template-version-comment.yml

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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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
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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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.nf-core.yml

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nextflow_config:
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- manifest.name
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- manifest.homePage
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nf_core_version: 3.3.2
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nf_core_version: 3.5.2
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repository_type: pipeline
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template:
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author: Damon-Lee B Pointon (@DLBPointon)
@@ -48,4 +48,4 @@ template:
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- seqera_platform
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- multiqc
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- rocrate
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version: 1.5.1
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version: 1.6.0

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