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Merge pull request #1384 from mahesh-panchal/master
Add Gitpod environment to nf-core tools
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‎.github/workflows/build_gitpod.yml‎

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name: nf-core gitpod build and push
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# Builds the docker image for gitpod and pushes it to DockerHub
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on:
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push:
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branches:
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- 'master'
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paths:
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- 'nf_core/gitpod/gitpod.Dockerfile'
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- '.github/workflows/build_gitpod.yml'
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jobs:
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push_to_registry:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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# Only run for the nf-core repo, for releases and merged PRs
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if: ${{ github.repository == 'nf-core/tools' }}
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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- name: Log in to Docker Hub
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_PASS }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v3
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with:
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images: nfcore/gitpod
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tags: |
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type=semver,pattern={{version}}
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type=raw,value=latest
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- name: Build and push Docker image
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uses: docker/build-push-action@v2
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with:
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context: .
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file: nf_core/gitpod/gitpod.Dockerfile
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}

‎.gitpod.yml‎

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image: nfcore/gitpod:latest
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tasks:
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- name: install current state of nf-core/tools
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command: |
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python -m pip install --upgrade -r requirements-dev.txt -e .
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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- codezombiech.gitignore # Language support for .gitignore files
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# - cssho.vscode-svgviewer # SVG viewer
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- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
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- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
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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

‎CHANGELOG.md‎

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* Remove base `Dockerfile` used for DSL1 pipeline container builds
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* Run tests with Python 3.10
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* [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions.
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* [#1384](https://github.com/nf-core/tools/pull/1384) Adds Gitpod environment and Dockerfile.
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* Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image.
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* Adds GH action to build and push Gitpod Docker image.
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* Adds Gitpod environment to template.
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* Adds Gitpod environment to tools with auto build of nf-core tool.
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### Modules
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‎nf_core/gitpod/gitpod.Dockerfile‎

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FROM gitpod/workspace-full
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USER root
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# Install Conda
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RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
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bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
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rm Miniconda3-latest-Linux-x86_64.sh
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ENV PATH="/opt/conda/bin:$PATH"
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RUN chown -R gitpod:gitpod /opt/conda
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USER gitpod
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# Install nextflow, nf-core, Mamba, and pytest-workflow
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RUN conda update -n base -c defaults conda && \
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conda install nextflow nf-core pytest-workflow mamba pip -n base -c conda-forge -c bioconda && \
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nextflow self-update && \
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conda config --add channels defaults && \
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conda config --add channels bioconda && \
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conda config --add channels conda-forge && \
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conda clean --all -f -y

‎nf_core/pipeline-template/.gitpod.yml‎

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image: nfcore/gitpod:latest
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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- codezombiech.gitignore # Language support for .gitignore files
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# - cssho.vscode-svgviewer # SVG viewer
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- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
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- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
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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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