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Merge branch 'dev' into nf-prov
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‎.devcontainer/devcontainer.json

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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
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"python.formatting.yapfPath": "/opt/conda/bin/yapf",
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"python.linting.flake8Path": "/opt/conda/bin/flake8",
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"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
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"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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"python.defaultInterpreterPath": "/opt/conda/bin/python"
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},
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// Add the IDs of extensions you want installed when the container is created.

‎.editorconfig

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This file was deleted.

‎.github/.coveragerc

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[run]
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omit = nf_core/pipeline-template/*
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omit = nf_core/*-template/*
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source = nf_core
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relative_files = True

‎.github/ISSUE_TEMPLATE/bug_report.yml

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description: Steps to reproduce the behaviour. Please paste the command and output from your terminal.
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render: console
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placeholder: |
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$ nf-core lint ...
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$ nf-core pipelines lint ...
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Some output where something broke
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@@ -37,5 +37,5 @@ body:
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
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* Python version _(eg. 3.10, 3.11)_
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* Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
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* Python version _(eg. 3.11, 3.12)_

‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -6,7 +6,7 @@ These are the most common things requested on pull requests (PRs).
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Remember that PRs should be made against the dev branch, unless you're preparing a release.
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Learn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md
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Learn more about contributing: https://github.com/nf-core/tools/tree/main/.github/CONTRIBUTING.md
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-->
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## PR checklist

‎.github/RELEASE_CHECKLIST.md

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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. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
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3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
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4. Check that modules/subworkflows in tempalte are up to date with the latest releases
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4. Check that modules/subworkflows in template are up to date with the latest releases
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5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
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6. Make sure all CI tests are passing!
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7. Create a PR from `dev` to `master`
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8. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
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7. Create a PR from `dev` to `main`
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8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
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9. Request review (2 approvals required)
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10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
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11. Merge the PR into `master`
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12. Wait for CI tests on the commit to passed
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13. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
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14. Create a new release copying the `CHANGELOG` for that release into the description section.
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10. Merge the PR into `main`
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11. Wait for CI tests on the commit to passed
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12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
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13. 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` and change the gitpod container to `nfcore/gitpod:dev`.
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5. Run `rich-codex` on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml) to regenerate docs screengrabs (actions `workflow_dispatch` button)

‎.github/actions/create-lint-wf/action.yml

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name: "Create and lint nf-core pipeline"
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description: "Create and lint nf-core pipeline"
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inputs:
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NXF_VER:
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description: "Nextflow version"
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required: true
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runs:
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using: "composite"
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steps:
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- name: go to subdirectory and change nextflow workdir
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shell: bash
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run: |
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mkdir -p create-lint-wf
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cd create-lint-wf
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export NXF_WORK=$(pwd)
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v2
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with:
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version: ${{ matrix.NXF_VER }}
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# Build a pipeline from the template
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- name: nf-core create
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shell: bash
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run: |
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mkdir -p create-lint-wf && cd create-lint-wf
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export NXF_WORK=$(pwd)
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nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
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# Try syncing it before we change anything
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- name: nf-core pipelines sync
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shell: bash
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run: nf-core --log-file log.txt pipelines sync --dir nf-core-testpipeline/
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working-directory: create-lint-wf
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# Run code style linting
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- name: run pre-commit
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shell: bash
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run: pre-commit run --all-files
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working-directory: create-lint-wf
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# Update modules to the latest version
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- name: nf-core modules update
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shell: bash
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run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
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working-directory: create-lint-wf
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# Remove TODO statements
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- name: remove TODO
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shell: bash
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run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
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working-directory: create-lint-wf
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# Uncomment includeConfig statement
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- name: uncomment include config
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shell: bash
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run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
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working-directory: create-lint-wf
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# Replace zenodo.XXXXXX to pass readme linting
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- name: replace zenodo.XXXXXX
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shell: bash
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run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
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working-directory: create-lint-wf
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# Add empty ro-crate file
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- name: add empty ro-crate file
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shell: bash
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run: touch nf-core-testpipeline/ro-crate-metadata.json
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working-directory: create-lint-wf
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# Run nf-core pipelines linting
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- name: nf-core pipelines lint
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shell: bash
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run: nf-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned
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working-directory: create-lint-wf
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- name: nf-core pipelines bump-version to release
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shell: bash
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run: nf-core --log-file log.txt pipelines bump-version --dir nf-core-testpipeline/ 1.1
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working-directory: create-lint-wf
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- name: nf-core pipelines lint in release mode
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shell: bash
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run: nf-core --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
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working-directory: create-lint-wf
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- name: Upload log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
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with:
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name: nf-core-log-file-${{ matrix.NXF_VER }}
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path: create-lint-wf/log.txt
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- name: nf-core modules install
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shell: bash
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run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
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working-directory: create-lint-wf
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- name: nf-core modules install gitlab
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shell: bash
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run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
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working-directory: create-lint-wf
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- name: nf-core modules list local
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shell: bash
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run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
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working-directory: create-lint-wf
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- name: nf-core modules list remote
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shell: bash
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run: nf-core --log-file log.txt modules list remote
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working-directory: create-lint-wf
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- name: nf-core modules list remote gitlab
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shell: bash
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run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
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working-directory: create-lint-wf

‎.github/renovate.json5

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{
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$schema: "https://docs.renovatebot.com/renovate-schema.json",
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extends: ["github>nf-core/ops//.github/renovate/default.json5"],
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ignorePaths: ["**/nf_core/pipeline-template/modules/nf-core/**"],
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baseBranches: ["dev"],
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packageRules: [
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{
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matchDatasources: ["docker"],
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matchPackageNames: ["python"],
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versioning: "pep440",
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},
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{
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matchDatasources: ["docker"],
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registryUrls: ["docker.io"],
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},
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],
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gitIgnoredAuthors: ["[email protected]"],
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}

‎.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 branch on the repository
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# It fails when someone tries to make a PR against the nf-core `main` 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: [main]
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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 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/tools'
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run: |
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# If the above check failed, post a comment on the PR explaining the failure
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@v1
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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 `main` 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/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
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The `main` branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to `main` are only allowed if they come from the [${{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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