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initial template build from nf-core/tools, version 2.14.1
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GallVp committed Aug 19, 2024
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20 changes: 20 additions & 0 deletions .devcontainer/devcontainer.json
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{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// 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"
},

// 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"]
}
}
}
42 changes: 3 additions & 39 deletions .editorconfig
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Expand Up @@ -8,7 +8,7 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{md,yml,yaml,html,css,scss,js,cff}]
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2

# These files are edited and tested upstream in nf-core/modules
Expand All @@ -18,52 +18,16 @@ end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset

[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset

# These files are edited and tested upstream in pfr/modules
[/modules/gallvp/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset

[/subworkflows/gallvp/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset

[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
[*.{py}]
# ignore python and markdown
[*.{py,md}]
indent_style = unset

# ignore perl
[*.{pl,pm}]
indent_size = unset

# ignore drawio
[*.drawio]
indent_size = unset

# ignore LICENSE
[LICENSE]
indent_size = unset
4 changes: 4 additions & 0 deletions .gitattributes
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*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
6 changes: 6 additions & 0 deletions .github/.dockstore.yml
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# Dockstore config version, not pipeline version
version: 1.2
workflows:
- subclass: nfl
primaryDescriptorPath: /nextflow.config
publish: True
118 changes: 118 additions & 0 deletions .github/CONTRIBUTING.md
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# PlantandFoodResearch/genepal: Contributing Guidelines

Hi there!
Many thanks for taking an interest in improving PlantandFoodResearch/genepal.

We try to manage the required tasks for PlantandFoodResearch/genepal using GitHub issues, you probably came to this page when creating one.
Please use the pre-filled template to save time.

However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)

## Contribution workflow

If you'd like to write some code for PlantandFoodResearch/genepal, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [PlantandFoodResearch/genepal issues](https://github.com/PlantandFoodResearch/genepal/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [PlantandFoodResearch/genepal repository](https://github.com/PlantandFoodResearch/genepal) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).

## Tests

You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:

```bash
nf-test test --profile debug,test,docker --verbose
```

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

There are typically two types of tests that run:

### Lint tests

`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

### Pipeline tests

Each `nf-core` pipeline should be set up with a minimal set of test-data.
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
If there are any failures then the automated tests fail.
These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.

## Patch

:warning: Only in the unlikely and regretful event of a release happening with a bug.

- On your own fork, make a new branch `patch` based on `upstream/master`.
- Fix the bug, and bump version (X.Y.Z+1).
- A PR should be made on `master` from patch to directly this particular bug.

## Pipeline contribution conventions

To make the PlantandFoodResearch/genepal code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.

### Adding a new step

If you wish to contribute a new step, please use the following coding standards:

1. Define the corresponding input channel into your new process from the expected previous process channel
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new parameters to `nextflow.config` with a default (see below).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.

### Default values

Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

### Default processes resource requirements

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.

### Naming schemes

Please use the following naming schemes, to make it easy to understand what is going where.

- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`

### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

## GitHub Codespaces

This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.

To get started:

- Open the repo in [Codespaces](https://github.com/PlantandFoodResearch/genepal/codespaces)
- Tools installed
- nf-core
- Nextflow

Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
54 changes: 54 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used
to launch the pipeline and the output from your terminal.
render: console
placeholder: "$ nextflow run ...
Some output where something broke
"
- type: textarea
id: files
attributes:
label: Relevant files
description: "Please drag and drop the relevant files here. Create a `.zip` archive
if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
in the directory where you launched the pipeline)_ as well as custom Nextflow
configuration files.
"
- type: textarea
id: system
attributes:
label: System information
description: "* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of PlantandFoodResearch/genepal _(eg. 1.1, 1.5, 1.8.2)_
"
11 changes: 11 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.yml
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name: Feature request
description: Suggest an idea for the PlantandFoodResearch/genepal pipeline
labels: enhancement
body:
- type: textarea
id: description
attributes:
label: Description of feature
description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
validations:
required: true
25 changes: 25 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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<!--
# PlantandFoodResearch/genepal pull request
Many thanks for contributing to PlantandFoodResearch/genepal!
Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
Learn more about contributing: [CONTRIBUTING.md](https://github.com/PlantandFoodResearch/genepal/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/PlantandFoodResearch/genepal/tree/master/.github/CONTRIBUTING.md)
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and authors/contributors).
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