Merge pull request #1384 from mahesh-panchal/master

Add Gitpod environment to nf-core tools

.github/workflows/build_gitpod.yml

@@ -0,0 +1,44 @@
+name: nf-core gitpod build and push
+# Builds the docker image for gitpod and pushes it to DockerHub
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - 'nf_core/gitpod/gitpod.Dockerfile'
+      - '.github/workflows/build_gitpod.yml'
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/tools' }}
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASS  }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: nfcore/gitpod
+          tags: |
+            type=semver,pattern={{version}}
+            type=raw,value=latest
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: nf_core/gitpod/gitpod.Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitpod.yml

@@ -0,0 +1,17 @@
+image: nfcore/gitpod:latest
+tasks:
+  - name: install current state of nf-core/tools
+    command: |
+      python -m pip install --upgrade -r requirements-dev.txt -e .
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code

CHANGELOG.md

@@ -63,6 +63,11 @@
 * Remove base `Dockerfile` used for DSL1 pipeline container builds
 * Run tests with Python 3.10
 * [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions.
+* [#1384](https://github.com/nf-core/tools/pull/1384) Adds Gitpod environment and Dockerfile.
+    * Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image.
+    * Adds GH action to build and push Gitpod Docker image.
+    * Adds Gitpod environment to template.
+    * Adds Gitpod environment to tools with auto build of nf-core tool.
 
 ### Modules
 

nf_core/gitpod/gitpod.Dockerfile

@@ -0,0 +1,23 @@
+FROM gitpod/workspace-full
+
+USER root
+
+# Install Conda
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
+    rm Miniconda3-latest-Linux-x86_64.sh
+
+ENV PATH="/opt/conda/bin:$PATH"
+
+RUN chown -R gitpod:gitpod /opt/conda
+
+USER gitpod
+
+# Install nextflow, nf-core, Mamba, and pytest-workflow
+RUN conda update -n base -c defaults conda && \
+    conda install nextflow nf-core pytest-workflow mamba pip -n base -c conda-forge -c bioconda && \
+    nextflow self-update && \
+    conda config --add channels defaults && \
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda clean --all -f -y

nf_core/pipeline-template/.gitpod.yml

@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code