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Add codespaces template for creating new repo's. #1957

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765ed75
Add codespaces template for creating new repo's.
vsmalladi Oct 18, 2022
c2a2e91
Update change log.
vsmalladi Oct 18, 2022
f9722a6
Update readme with codepsaces.
vsmalladi Oct 18, 2022
20ca392
Update README.md
vsmalladi Oct 18, 2022
492d6f5
Change to absolute url
vsmalladi Oct 19, 2022
dc4e4d6
Add nextflow extension pack.
vsmalladi Oct 27, 2022
e8f0502
Update syntax.
vsmalladi Oct 27, 2022
d8bd517
Moved section to root Contributing directory.
vsmalladi Oct 27, 2022
3817949
Make more parity with Gitpod.
vsmalladi Oct 27, 2022
862fa6b
Make more parity with Gitpod.
vsmalladi Oct 27, 2022
cc144b3
Add a codspaces for the tools repo.
vsmalladi Oct 27, 2022
f4205ad
Merge branch 'dev' into dev
vsmalladi Oct 28, 2022
efee035
Sync gitpod and codespaces.
vsmalladi Oct 28, 2022
6a77c35
Merge branch 'dev' of github.com:vsmalladi/tools into dev
vsmalladi Oct 28, 2022
3274319
Fix build of nfcore tools.
vsmalladi Oct 28, 2022
1f6a256
Sync gitpod and codespaces.
vsmalladi Oct 28, 2022
430463d
Merge branch 'dev' into dev
vsmalladi Oct 28, 2022
a51bfec
[automated] Fix code linting
nf-core-bot Oct 28, 2022
ae7fae1
Remove redundant extensions
vsmalladi Nov 2, 2022
c6fb549
Remove redundant extensions
vsmalladi Nov 2, 2022
e604cb7
Update CONTRIBUTING.md
vsmalladi Nov 2, 2022
2ed9ecf
Merge branch 'dev' into dev
vsmalladi Nov 2, 2022
2a16a60
Merge branch 'dev' into dev
mahesh-panchal Nov 3, 2022
1539777
[automated] Fix code linting
nf-core-bot Nov 3, 2022
6654027
Apply suggestions from code review
ewels Nov 3, 2022
0146a89
Add Codespaces instructions to pipeline template CONTRIBUTING too
ewels Nov 3, 2022
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39 changes: 39 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../",
"remoteUser": "gitpod",

// 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",
"nf-core.nf-core-extensionpack",
"codezombiech.gitignore",
"esbenp.prettier-vscode",
"EditorConfig.EditorConfig",
"Gruntfuggly.todo-tree",
"mechatroner.rainbow-csv",
"derwat.indent-rainbow",
"streetsidesoftware.code-spell-checker"
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]
}
}
}
16 changes: 16 additions & 0 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -127,3 +127,19 @@ You can replicate this process locally with the following commands:
nf-core create -n testpipeline -d "This pipeline is for testing"
nf-core lint nf-core-testpipeline
```

## 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)
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# To get started:
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- Open the repo in [Codespaces](https://github.com/{{ name }})/codespaces)
- Tools installed
- nf-core
- nextflow
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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))
- Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))

### Linting
Expand Down
38 changes: 38 additions & 0 deletions nf_core/pipeline-template/.devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",

// 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",
"nf-core.nf-core-extensionpack",
"codezombiech.gitignore",
"esbenp.prettier-vscode",
"EditorConfig.EditorConfig",
"Gruntfuggly.todo-tree",
"mechatroner.rainbow-csv",
"derwat.indent-rainbow",
"streetsidesoftware.code-spell-checker"
]
}
}
}