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Merge pull request #3 from AlexVCaron/fix/template_placeholders
Update template
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‎.editorconfig

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@@ -28,10 +28,10 @@ indent_style = unset
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[/assets/email*]
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indent_size = unset
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# ignore Readme
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[README.md]
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indent_style = unset
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# ignore python
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset
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# ignore ro-crate metadata files
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[**/ro-crate-metadata.json]
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insert_final_newline = unset

‎.github/CONTRIBUTING.md

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# nf/tractoflow: Contributing Guidelines
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# `scilus/nf-tractoflow`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf/tractoflow.
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Many thanks for taking an interest in improving scilus/nf-tractoflow.
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We try to manage the required tasks for nf/tractoflow using GitHub issues, you probably came to this page when creating one.
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We try to manage the required tasks for scilus/nf-tractoflow using GitHub issues, you probably came to this page when creating one.
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Please use the pre-filled template to save time.
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However, don't be put off by this template - other more general issues and suggestions are welcome!
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Contributions to the code are even more welcome ;)
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## Contribution workflow
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If you'd like to write some code for nf/tractoflow, the standard workflow is as follows:
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If you'd like to write some code for scilus/nf-tractoflow, the standard workflow is as follows:
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1. Check that there isn't already an issue about your idea in the [nf/tractoflow issues](https://github.com/nf/tractoflow/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf/tractoflow repository](https://github.com/nf/tractoflow) to your GitHub account
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1. Check that there isn't already an issue about your idea in the [scilus/nf-tractoflow issues](https://github.com/scilus/nf-tractoflow/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [scilus/nf-tractoflow repository](https://github.com/scilus/nf-tractoflow) to your GitHub account
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3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
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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).
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4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
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5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
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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/).
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### Lint tests
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`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
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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.
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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 pipelines lint <pipeline-directory>` command.
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If any failures or warnings are encountered, please follow the listed URL for more documentation.
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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- On your own fork, make a new branch `patch` based on `upstream/master`.
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- A PR should be made on `master` from patch to directly this particular bug.
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Pipeline contribution conventions
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To make the nf/tractoflow 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.
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To make the `scilus/nf-tractoflow` 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.
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### Adding a new step
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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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1. Define the corresponding input channel into your new process from the expected previous process channel.
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new parameters to `nextflow.config` with a default (see below).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
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6. Add sanity checks and validation for all relevant parameters.
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7. Perform local tests to validate that the new code works as expected.
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8. If applicable, add a new test command in `.github/workflow/ci.yml`.
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
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Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
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### Default processes resource requirements
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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.
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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/main/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.
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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.
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### Nextflow version bumping
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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]`
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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 pipelines bump-version --nextflow . [min-nf-version]`
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### Images and figures
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To get started:
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- Open the repo in [Codespaces](https://github.com/nf/tractoflow/codespaces)
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- Open the repo in [Codespaces](https://github.com/scilus/nf-tractoflow/codespaces)
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- Tools installed
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- nf-core
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- Nextflow

‎.github/ISSUE_TEMPLATE/bug_report.yml

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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of the bug
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used
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to launch the pipeline and the output from your terminal.
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render: console
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placeholder: '$ nextflow run ...
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Some output where something broke
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'
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: 'Please drag and drop the relevant files here. Create a `.zip` archive
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if the extension is not allowed.
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Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
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in the directory where you launched the pipeline)_ as well as custom Nextflow
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configuration files.
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'
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- type: textarea
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id: system
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attributes:
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label: System information
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description: '* Nextflow version _(eg. 23.04.0)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
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or Apptainer)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf/tractoflow _(eg. 1.1, 1.5, 1.8.2)_
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'
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- type: textarea
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id: description
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attributes:
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label: Description of the bug
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
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render: console
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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: |
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Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
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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.
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- type: textarea
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id: system
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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 23.04.0)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of scilus/nf-tractoflow _(eg. 1.1, 1.5, 1.8.2)_

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Suggest an idea for the nf/tractoflow pipeline
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description: Suggest an idea for the scilus/nf-tractoflow pipeline
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body:
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- type: textarea

‎.github/PULL_REQUEST_TEMPLATE.md

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<!--
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# nf/tractoflow pull request
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# scilus/nf-tractoflow pull request
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Many thanks for contributing to nf/tractoflow!
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Many thanks for contributing to scilus/nf-tractoflow!
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Please fill in the appropriate checklist below (delete whatever is not relevant).
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These are the most common things requested on pull requests (PRs).
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Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf/tractoflow/tree/master/.github/CONTRIBUTING.md)
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/scilus/nf-tractoflow/tree/master/.github/CONTRIBUTING.md)
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-->
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## PR checklist
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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf/tractoflow/tree/master/.github/CONTRIBUTING.md)
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/scilus/nf-tractoflow/tree/master/.github/CONTRIBUTING.md)
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- [ ] Make sure your code lints (`nf-core pipelines lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.

‎.github/workflows/branch.yml

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name: nf-core branch protection
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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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# This workflow is triggered on PRs to `main`/`master` branch on the repository
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# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
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on:
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branches:
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- main
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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# PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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if: github.repository == 'nf/tractoflow'
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if: github.repository == 'scilus/nf-tractoflow'
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf/tractoflow ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == scilus/nf-tractoflow ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
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with:
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## This PR is against the `master` branch :x:
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## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
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* Do not close this PR
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* Click _Edit_ and change the `base` to `dev`
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Hi @${{ github.event.pull_request.user.login }},
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
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The `master` branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
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The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
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Note that even after this, the test will continue to show as failing until you push a new commit.

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