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Merge pull request #219 from qbic-pipelines/dev
Release 2.2
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‎.editorconfig

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@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml,html,css,scss,js,cff}]
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[*.{md,yml,yaml,html,css,scss,js}]
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indent_size = 2
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# These files are edited and tested upstream in nf-core/modules

‎.github/CONTRIBUTING.md

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# qbic-pipelines/rnadeseq: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/rnadeseq.
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Many thanks for taking an interest in improving qbic-pipelines/rnadeseq.
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We try to manage the required tasks for nf-core/rnadeseq using GitHub issues, you probably came to this page when creating one.
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We try to manage the required tasks for qbic-pipelines/rnadeseq using GitHub issues, you probably came to this page when creating one.
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Please use the pre-filled template to save time.
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However, don't be put off by this template - other more general issues and suggestions are welcome!
@@ -13,8 +13,8 @@ Contributions to the code are even more welcome ;)
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If you'd like to write some code for qbic-pipelines/rnadeseq, the standard workflow is as follows:
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1. Check that there isn't already an issue about your idea in the [nf-core/rnadeseq issues](https://github.com/nf-core/rnadeseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/rnadeseq repository](https://github.com/nf-core/rnadeseq) to your GitHub account
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1. Check that there isn't already an issue about your idea in the [qbic-pipelines/rnadeseq issues](https://github.com/qbic-pipelines/rnadeseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [qbic-pipelines/rnadeseq repository](https://github.com/qbic-pipelines/rnadeseq) to your GitHub account
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3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
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4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
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5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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## GitHub Codespaces
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This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
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To get started:
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- Open the repo in [Codespaces](https://github.com/qbic-pipelines/rnadeseq/codespaces)
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- Tools installed
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- nf-core
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- Nextflow
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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)

‎.github/ISSUE_TEMPLATE/bug_report.yml

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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 22.10.1)_
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* Nextflow version _(eg. 23.04.0)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of qbic-pipelines/rnadeseq _(eg. 1.1, 1.5, 1.8.2)_

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Suggest an idea for the nf-core/rnadeseq pipeline
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description: Suggest an idea for the qbic-pipelines/rnadeseq pipeline
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labels: enhancement
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body:
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- type: textarea

‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/qbic-pipelin
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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnadeseq/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/rnadeseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/qbic-pipelines/rnadeseq/tree/master/.github/CONTRIBUTING.md)
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.

‎.github/workflows/awsfulltest.yml

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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@v3
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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
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadeseq/work-${{ github.sha }}
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadeseq/results-${{ github.sha }}"
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}
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profiles: test_full,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3
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profiles: test_full
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json

‎.github/workflows/awstest.yml

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steps:
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# Launch workflow using Tower CLI tool action
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- name: Launch workflow via tower
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uses: nf-core/tower-action@v3
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadeseq/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadeseq/results-test-${{ github.sha }}"
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}
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profiles: test,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3
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profiles: test
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: |
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tower_action_*.log
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tower_action_*.json

‎.github/workflows/ci.yml

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NXF_ANSI_LOG: false
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CAPSULE_LOG: none
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concurrency:
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group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
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cancel-in-progress: true
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jobs:
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test:
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name: Run pipeline with test data
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matrix:
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# Nextflow versions
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NXF_VER:
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- "22.10.1"
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- "23.04.0"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v4
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environment.yml
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- name: Build new docker image
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if: env.MATCHED_FILES
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
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run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2
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# Change the version above and the third version below before/after release
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- name: Pull docker image
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if: ${{ !env.MATCHED_FILES }}
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run: |
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docker pull qbicpipelines/rnadeseq:dev
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
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docker pull ghcr.io/qbic-pipelines/rnadeseq:dev
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docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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name: Test workflow parameters
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runs-on: ubuntu-latest
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env:
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NXF_VER: "22.10.1"
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NXF_VER: "23.04.0"
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NXF_ANSI_LOG: false
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strategy:
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# This tells github to continue running other profile tests if some tests fail (default cancels all tests upon failure)
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"test_contrast_list",
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"test_no_multiqc",
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"test_relevel",
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"test_smrnaseq",
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"test_star_rsem",
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"test_star_salmon",
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"test_use_vst",
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]
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v4
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environment.yml
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- name: Build new docker image
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
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run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2
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# Change the version above and the third version below before/after release
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- name: Pull docker image
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run: |
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docker pull qbicpipelines/rnadeseq:dev
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
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docker pull ghcr.io/qbic-pipelines/rnadeseq:dev
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docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1

‎.github/workflows/clean-up.yml

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name: "Close user-tagged issues and PRs"
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on:
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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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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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- uses: actions/stale@v7
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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."
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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/fix-linting.yml

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id: prettier_status
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "name=result::pass" >> $GITHUB_OUTPUT
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echo "result=pass" >> $GITHUB_OUTPUT
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else
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echo "name=result::fail" >> $GITHUB_OUTPUT
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echo "result=fail" >> $GITHUB_OUTPUT
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fi
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- name: Run 'prettier --write'

‎.github/workflows/linting.yml

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- uses: actions/setup-python@v4
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with:
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python-version: "3.8"
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architecture: "x64"
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- name: Install dependencies

‎.github/workflows/push_dockerhub.yml

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‎.github/workflows/push_github_container_reg.yml

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name: Docker push
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# This builds the docker image and pushes it to GHCR
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# Runs on qbic-pipelines repo releases and push event to 'dev' branch (PR merges)
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on:
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push:
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branches:
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- dev
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release:
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types: [published]
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jobs:
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push_github:
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name: Push new Docker image to GHCR
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runs-on: ubuntu-latest
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# Only run for the qbic-pipelines repo, for releases and merged PRs
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if: ${{ github.repository == 'qbic-pipelines/rnadeseq' }}
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Build new docker image
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run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:latest
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- name: Log in to registry
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# Update the personal access token to GITHUB_TOKEN
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u $ --password-stdin
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- name: Push image to GHCR (dev)
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if: ${{ github.event_name == 'push' }}
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run: |
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docker tag ghcr.io/qbic-pipelines/rnadeseq:latest ghcr.io/qbic-pipelines/rnadeseq:dev
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docker push ghcr.io/qbic-pipelines/rnadeseq:dev
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- name: Push image to GHCR (release)
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if: ${{ github.event_name == 'release' }}
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run: |
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docker tag ghcr.io/qbic-pipelines/rnadeseq:latest ghcr.io/qbic-pipelines/rnadeseq:${{ github.event.release.tag_name }}
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docker push ghcr.io/qbic-pipelines/rnadeseq:${{ github.event.release.tag_name }}

‎.gitpod.yml

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image: nfcore/gitpod:latest
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tasks:
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- name: Update Nextflow and setup pre-commit
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command: |
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pre-commit install --install-hooks
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nextflow self-update
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack

‎.nf-core.yml

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repository_type: pipeline
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- .github/CONTRIBUTING.md
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- .github/ISSUE_TEMPLATE/config.yml
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- .github/workflows/awsfulltest.yml
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- .github/workflows/awstest.yml
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- .github/workflows/push_dockerhub.yml
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- assets/multiqc_config.yaml
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- assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
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- bin/markdown_to_html.r
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multiqc_config:
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- report_comment # otherwise throws error: multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'. │
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repository_type: pipeline

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v2.7.1"
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hooks:
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- id: prettier

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