Add codespaces template for creating new repo's.

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Fix lint warnings for `samplesheet_check.nf` module
+- Add codespaces template ([#1957](https://github.com/nf-core/tools/pull/1957))
 
 ### Linting
 

nf_core/pipeline-template/.devcontainer/Dockerfile

@@ -0,0 +1,21 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3-anaconda/.devcontainer/base.Dockerfile
+
+FROM mcr.microsoft.com/vscode/devcontainers/anaconda:0-3
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+RUN conda install -c bioconda nextflow
+RUN pip install nf-core
+

nf_core/pipeline-template/.devcontainer/add-notice.sh

@@ -0,0 +1,20 @@
+# Display a notice when not running in GitHub Codespaces
+
+cat << 'EOF' > /usr/local/etc/vscode-dev-containers/conda-notice.txt
+When using "conda" from outside of GitHub Codespaces, note the Anaconda repository 
+contains restrictions on commercial use that may impact certain organizations. See
+https://aka.ms/vscode-remote/conda/anaconda
+
+EOF
+
+notice_script="$(cat << 'EOF'
+if [ -t 1 ] && [ "${IGNORE_NOTICE}" != "true" ] && [ "${TERM_PROGRAM}" = "vscode" ] && [ "${CODESPACES}" != "true" ] && [ ! -f "$HOME/.config/vscode-dev-containers/conda-notice-already-displayed" ]; then
+    cat "/usr/local/etc/vscode-dev-containers/conda-notice.txt"
+    mkdir -p "$HOME/.config/vscode-dev-containers"
+    ((sleep 10s; touch "$HOME/.config/vscode-dev-containers/conda-notice-already-displayed") &)
+fi
+EOF
+)"
+
+echo "${notice_script}" | tee -a /etc/bash.bashrc >> /etc/zsh/zshrc
+

nf_core/pipeline-template/.devcontainer/devcontainer.json

@@ -0,0 +1,55 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3-anaconda
+{
+	"name": "Anaconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile",
+		"args": {
+			"NODE_VERSION": "lts/*"
+		}
+	},
+
+	// Configure tool-specific properties.
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": { 
+				"python.defaultInterpreterPath": "/opt/conda/bin/python",
+				"python.linting.enabled": true,
+				"python.linting.pylintEnabled": true,
+				"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+				"python.formatting.yapfPath": "/opt/conda/bin/yapf",
+				"python.linting.flake8Path": "/opt/conda/bin/flake8",
+				"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+				"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+				"python.linting.pylintPath": "/opt/conda/bin/pylint"
+			},
+
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-python.python",
+				"ms-python.vscode-pylance"
+			]
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "python --version",
+
+	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode",
+	"features": {
+		"docker-in-docker": "20.10",
+		"git": "os-provided",
+		"ghcr.io/devcontainers/features/conda:1": {},
+		"ghcr.io/devcontainers/features/docker-from-docker:1": {},
+		"ghcr.io/devcontainers/features/git:1": {}
+	}
+}
+
+

nf_core/pipeline-template/.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file copied into the container along with environment.yml* from the parent
+folder. This file is included to prevents the Dockerfile COPY instruction from 
+failing if no environment.yml is found.

nf_core/pipeline-template/README.md

@@ -73,6 +73,19 @@ The results obtained from the full-sized test can be viewed on the [nf-core webs
 
 {% if branded -%}
 
+## Codespaces
+This repo includes a devcontainer configuration which will create a GitHub Codespace for Nextflow development!
+
+Devcontainer specs:
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)
+
+# Getting started
+- Open the repo in [Codespaces](../../codespaces)
+- Tools installed
+   - nf-core
+   - nextflow
+
 ## Documentation
 
 The {{ name }} pipeline comes with documentation about the pipeline [usage](https://nf-co.re/{{ short_name }}/usage), [parameters](https://nf-co.re/{{ short_name }}/parameters) and [output](https://nf-co.re/{{ short_name }}/output).