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💚 ci(pre-commit): replace prettier workflow with pre-commit (#501)
This replaces the previous prettier github workflow with a pre-commit run which will ensure consistency between local pre-commit runs and our ci. In addition, this removes the .pretterrc.yml file and replaces it with an editorconfig file that matches the config used in nf-core repos. Finally, this applies the new editorconfig settings to the repo as a whole.
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‎.devcontainer/Dockerfile‎

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FROM ghcr.io/nextflow-io/training:latest
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ENV NXF_VER=24.10.0
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ENV NXF_EDGE=0
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ENV NXF_EDGE=0

‎.editorconfig‎

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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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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}]
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indent_size = 2
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset

‎.github/workflows/docker.yml‎

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name: Build GitPod Docker image
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on:
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pull_request:
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push:
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branches: [master]
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release:
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types: [published]
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pull_request:
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push:
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branches: [master]
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release:
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types: [published]
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jobs:
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push_to_registry:
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if: github.repository == 'nextflow-io/training'
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name: Build + Push Gitpod Docker image
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v4
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push_to_registry:
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if: github.repository == 'nextflow-io/training'
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name: Build + Push Gitpod Docker image
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v4
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build / push latest image
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uses: docker/build-push-action@v5
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if: github.event_name != 'release'
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with:
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file: .github/gitpod.Dockerfile
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push: ${{ github.event_name == 'push' }}
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tags: ghcr.io/nextflow-io/training:latest
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- name: Build / push latest image
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uses: docker/build-push-action@v5
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if: github.event_name != 'release'
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with:
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file: .github/gitpod.Dockerfile
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push: ${{ github.event_name == 'push' }}
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tags: ghcr.io/nextflow-io/training:latest
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- name: Push release image
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uses: docker/build-push-action@v5
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if: github.event_name == 'release'
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with:
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file: .github/gitpod.Dockerfile
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push: true
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tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}
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- name: Push release image
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uses: docker/build-push-action@v5
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if: github.event_name == 'release'
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with:
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file: .github/gitpod.Dockerfile
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push: true
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tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}

‎.github/workflows/mkdocs-docker.yml‎

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name: Build mkdocs docker image
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on:
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pull_request:
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push:
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branches: [master]
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pull_request:
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push:
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branches: [master]
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jobs:
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mkdocs_docker:
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if: github.repository == 'nextflow-io/training'
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name: Build + push mkdocs docker image
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v4
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mkdocs_docker:
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if: github.repository == 'nextflow-io/training'
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name: Build + push mkdocs docker image
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v4
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build / push latest image
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uses: docker/build-push-action@v5
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with:
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file: .github/mkdocs.Dockerfile
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push: ${{ github.event_name == 'push' }}
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tags: ghcr.io/nextflow-io/training-mkdocs:latest
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- name: Build / push latest image
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uses: docker/build-push-action@v5
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with:
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file: .github/mkdocs.Dockerfile
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push: ${{ github.event_name == 'push' }}
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tags: ghcr.io/nextflow-io/training-mkdocs:latest

‎.github/workflows/precommit.yml‎

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name: Pre-commit checks
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on:
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push:
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pull_request:
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jobs:
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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@v3
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- uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- uses: pre-commit/[email protected]

‎.github/workflows/prettier.yml‎

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This file was deleted.

‎.gitpod.yml‎

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checkoutLocation: gitpod
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github:
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prebuilds:
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# enable for the master/default branch (defaults to true)
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master: true
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# enable for all branches in this repo (defaults to false)
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branches: false
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# enable for pull requests coming from this repo (defaults to true)
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pullRequests: true
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# enable for pull requests coming from forks (defaults to false)
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pullRequestsFromForks: true
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# add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
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addComment: true
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# add a "Review in Gitpod" button to pull requests (defaults to false)
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addBadge: false
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prebuilds:
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# enable for the master/default branch (defaults to true)
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master: true
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# enable for all branches in this repo (defaults to false)
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branches: false
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# enable for pull requests coming from this repo (defaults to true)
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pullRequests: true
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# enable for pull requests coming from forks (defaults to false)
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pullRequestsFromForks: true
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# add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
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addComment: true
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# add a "Review in Gitpod" button to pull requests (defaults to false)
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addBadge: false
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# See .github/Dockerfile
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image: ghcr.io/nextflow-io/training:latest
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tasks:
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- before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
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- before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
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- name: Start web server
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command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow
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- name: Start web server
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command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow
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- name: Load Nextflow Tutorial
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command: docker pull -q nextflow/rnaseq-nf
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- name: Load Nextflow Tutorial
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command: docker pull -q nextflow/rnaseq-nf
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- name: Start Nextflow Tutorial
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env:
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NXF_HOME: "/workspace/gitpod/.nextflow"
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command: |
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cd hello-nextflow
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source $HOME/.bashrc
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export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
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unset JAVA_TOOL_OPTIONS
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clear
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- name: Start Nextflow Tutorial
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env:
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NXF_HOME: "/workspace/gitpod/.nextflow"
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command: |
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cd hello-nextflow
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source $HOME/.bashrc
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export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
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unset JAVA_TOOL_OPTIONS
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clear
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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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- 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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- ms-vscode.live-server
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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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- 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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- ms-vscode.live-server

‎.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: "v3.1.0"
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hooks:
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- id: prettier
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additional_dependencies:
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- [email protected]
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v3.1.0"
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hooks:
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- id: prettier
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additional_dependencies:
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- [email protected]
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "2.7.3"
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hooks:
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- id: editorconfig-checker
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alias: ec
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "2.7.3"
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hooks:
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- id: editorconfig-checker
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alias: ec
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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exclude_types:
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- svg
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- id: end-of-file-fixer
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exclude_types:
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- svg
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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exclude_types:
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- svg
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- id: end-of-file-fixer
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exclude_types:
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- svg

‎.prettierrc‎

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‎CONTRIBUTING.md‎

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Table of contents:
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- [Contributing](#contributing)
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- [Contribution model](#contribution-model)
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- [Installation](#installation)
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- [Docker](#docker)
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- [Python](#python)
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- [Social cards](#social-cards)
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- [Figures \& diagrams](#figures--diagrams)
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- [Content style and formatting](#content-style-and-formatting)
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- [Formatting / linting](#formatting--linting)
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- [Admonitions](#admonitions)
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- [Known limitations](#known-limitations)
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- [Code annotations](#code-annotations)
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- [Word highlighting](#word-highlighting)
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- [TODO / FIXME](#todo--fixme)
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- [Contributing](#contributing)
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- [Contribution model](#contribution-model)
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- [Installation](#installation)
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- [Docker](#docker)
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- [Python](#python)
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- [Social cards](#social-cards)
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- [Figures \& diagrams](#figures--diagrams)
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- [Content style and formatting](#content-style-and-formatting)
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- [Formatting / linting](#formatting--linting)
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- [Admonitions](#admonitions)
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- [Known limitations](#known-limitations)
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- [Code annotations](#code-annotations)
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- [Word highlighting](#word-highlighting)
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- [TODO / FIXME](#todo--fixme)
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## Contribution model
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```yaml
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extra:
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# Announcement banner for upcoming training
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announcement:
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active: false
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date_text: March 5-6, 2024
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register_url: https://nf-co.re/events/2024/training-foundational-march
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# Announcement banner for upcoming training
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announcement:
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active: false
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date_text: March 5-6, 2024
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register_url: https://nf-co.re/events/2024/training-foundational-march
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```
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If you need more customisation, edit `docs/assets/overrides/main.html`
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We use admonitions extensively to make certain pieces of content stand out.
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Please see the [official docs](https://squidfunk.github.io/mkdocs-material/reference/admonitions/) for an explanation.
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- Note that we have two custom admonitions: `exercise` and `result` (alias `solution`).
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- `!!!` does a regular admonition, `???` makes it collapsed (click to expand).
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- Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake.
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- Note that we have two custom admonitions: `exercise` and `result` (alias `solution`).
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- `!!!` does a regular admonition, `???` makes it collapsed (click to expand).
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- Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake.
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## Known limitations
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A list of key ones also included here:
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- Remove plugin install from Phil's GitHub fork in `requirements.txt` and `.github/mkdocs.Dockerfile` when [this PR](https://github.com/timvink/mkdocs-enumerate-headings-plugin/pull/33) is merged
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- Remove plugin install from Phil's GitHub fork in `requirements.txt` and `.github/mkdocs.Dockerfile` when [this PR](https://github.com/timvink/mkdocs-enumerate-headings-plugin/pull/33) is merged

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