Move CONTRIBUTING.md to docs/, review and update text, and add pipline-specific conventions section

CHANGELOG.md

@@ -31,6 +31,7 @@
 
 - Change GitHub Codespaces badge style ([#3869](https://github.com/nf-core/tools/pull/3869) and [#3873](https://github.com/nf-core/tools/pull/3873))
 - Update multiqc to 1.32 ([#3878](https://github.com/nf-core/tools/pull/3878))
+- Move CONTRIBUTING.md to docs/, review and update text, and add pipeline-specific conventions section ([#3903](https://github.com/nf-core/tools/pull/3903))
 
 ### Linting
 

nf_core/pipeline-template/docs/CONTRIBUTING.md

@@ -0,0 +1,186 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `{{ name }}`: Contributing Guidelines
+
+Hi there!
+Many thanks for taking an interest in improving {{ name }}.
+
+This page describes the recommended nf-core way for contributing to both {{ name }} and nf-core pipelines in general.
+
+- [General contribution guidelines](#general-contribution-guidelines): for common procedures or guides across all nf-core pipelines.
+- [Pipeline specific contribution guidelines](#pipeline-specific-contribution-guidelines): for any procedures or guides specific to the development conventions of {{ name }}.
+
+{% if is_nfcore -%}
+
+> [!NOTE]
+> If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+{% endif -%}
+
+## General contribution guidelines
+
+### Contribution quick start
+
+If you'd like to write some code for {{ name }}, the standard workflow is as follows:
+
+- [ ] Make sure you have Nextflow, nf-core tools, and nf-test installed - see the [nf-core/tools repository](https://github.com/nf-core/tools).
+- [ ] Check that there isn't already an issue about your idea in the [{{ name }} issues](https://github.com/{{ name }}/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this.
+- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [{{ name }} repository](https://github.com/{{ name }}) to your GitHub account.
+- [ ] Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions), ideally on a branch
+- [ ] - If you are fixing a major bug, please using a branch nmmed `patch` and see the [Patch](#patch) section below.
+- [ ] Update any relevant documentation within the `docs/` folder and use nf-core/tools to update `nextflow_schema.json` using nf-core/tools.
+- [ ] [Lint](#lint-tests) your code using nf-core/tools
+- [ ] Run and/or update tests as appropriate (see [Tests](#tests) section below).
+- [ ] Submit a Pull Request against the `dev` branch and request 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/).
+
+{% if is_nfcore -%}
+
+### Getting help
+
+For further information/help, please consult the [{{ name }} documentation](https://nf-co.re/{{ short_name }}/usage) and don't hesitate to get in touch on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+{% endif -%}
+
+{%- if codespaces %}
+
+### 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/{{ name }}/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+  {%- endif %}
+
+### Tests
+
+{% if test_config -%}
+You have the option to test your changes locally by running the pipeline using nf-test.
+We recommend to use the `--verbose` flag to see the Nextflow console log output in addition to nf-test's own output.
+
+```bash
+nf-test test --tag test --profile +docker --verbose
+```
+
+{% endif -%}
+
+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.
+
+{% if test_config %}There are typically two types of tests that run:{% endif %}
+
+#### Lint tests
+
+`nf-core` has a [set of guidelines](https://nf-co.re/docs/contributing/guidelines) which all pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, you can use the nf-core/tools package to run the linting locally with the command.
+
+```bash
+nf-core pipelines lint <pipeline-directory>
+```
+
+If any failures or warnings are encountered, please follow the listed URL for more documentation.
+The full list of tests can be seen [here](https://nf-co.re/docs/nf-core-tools/api_reference/latest/pipeline_lint_tests/actions_awsfulltest).
+
+{%- if test_config %}
+
+#### 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.
+{%- endif %}
+
+### 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/main` or `upstream/master`.
+- [ ] Fix the bug, and use nf-core tools to bump version to the next semantic version e.g., `1.2.3` -> `1.2.4`.
+- [ ] Open a pull-request from `patch` directly to `main`/`master` with the changes.
+
+### Pipeline contribution conventions
+
+To make the `{{ name }}` 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 to the pipeline, please use the following general nf-core coding procedure.
+Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines):
+
+- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel.
+- [ ] Install a module using nf-core tools, or write a local module (check [info about resources](#default-processes-resource-requirements)), and add it to the target `<workflow>.nf`.
+- [ ] Define the output channel if needed (see below), mixing both the version output channel into `ch_versions` and relevant files into `ch_multiqc`.
+- [ ] Add any new/update parameters to `nextflow.config` with a [default](#default-values) (see below).
+- [ ] Add any new/update parameters to `nextflow_schema.json` with help text using [nf-core/tools](#default-values).
+- [ ] Add validation for all relevant parameters to the pipeline`utilisation section of`utils*nfcore*{{ shortname }}\_pipeline/main.nf` subworkflow.
+- [ ] Perform local tests to validate that the new code works as expected.
+- [ ] If applicable, add a new test in the `tests` directory.
+- [ ] Update `usage.md`, `output.md`, `citation.md` docs as appropriate.
+- [ ] [Lint](lint) the code using nf-core/tools
+- [ ] Update any diagrams or pipeline images as necessary
+      {%- if multiqc %}
+- [ ]. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. - [ ] applicable, add a [MultiQC](https://seqera.io/multiqc/) module.
+- [ ]. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+  {%- endif %}
+
+If you need to update the minimum required Nextflow version, please see the [Nextflow version bumping](#nextflow-version-bumping) section below.
+
+#### Channel naming schemes
+
+Please use the following naming schemes for channels, 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>`
+
+#### Default values
+
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
+
+Once there, use:
+
+```bash
+nf-core pipelines schema build
+```
+
+To update `nextflow_schema.json`.
+
+#### Default processes resource requirements
+
+If writing a local module, you should specify a default set of resource requirements for the process.
+
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`.
+These should generally be specified with generic `withLabel:` selectors, so they can be shared across multiple processes/steps of the pipeline.
+
+nf-core provides a set of standard labels that should be followed where possible, and can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
+These labels have resource defaults for a single core-process, a module requiring use of a GPU, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+
+The process resources should be passed on to the tool dynamically within the process using the `${task.cpus}` Nextflow variable, and where necessary the `${task.memory}` variable, in the command of the `script:` block (see example [here](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+
+#### Images and figures
+
+For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/docs/guidelines/graphic_design/overview).
+
+#### 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:
+
+```bash
+nf-core pipelines bump-version --nextflow . [min-nf-version]
+```
+
+## Pipeline specific contribution guidelines
+
+<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->