nf-cmgg
diff --git a/‎.devcontainer/devcontainer.json
+20 b/‎.devcontainer/devcontainer.json
+20
diff --git a/‎.editorconfig
+15-2 b/‎.editorconfig
+15-2
diff --git a/‎.gitattributes
+1 b/‎.gitattributes
+1
diff --git a/‎.github/CONTRIBUTING.md
+33-8 b/‎.github/CONTRIBUTING.md
+33-8
diff --git a/‎.github/ISSUE_TEMPLATE/bug_report.yml
+20-17 b/‎.github/ISSUE_TEMPLATE/bug_report.yml
+20-17
diff --git a/‎.github/ISSUE_TEMPLATE/config.yml
+7 b/‎.github/ISSUE_TEMPLATE/config.yml
+7
diff --git a/‎.github/ISSUE_TEMPLATE/feature_request.yml
+1-1 b/‎.github/ISSUE_TEMPLATE/feature_request.yml
+1-1
diff --git a/‎.github/PULL_REQUEST_TEMPLATE.md
+7-5 b/‎.github/PULL_REQUEST_TEMPLATE.md
+7-5
diff --git a/‎.github/workflows/branch.yml
+3-3 b/‎.github/workflows/branch.yml
+3-3
diff --git a/‎.github/workflows/build-docs.yml
+38 b/‎.github/workflows/build-docs.yml
+38
@@ -0,0 +1,20 @@
+{
+    "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"]
+        }
+    }
+}
@@ -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
@@ -18,7 +18,20 @@ 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
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py,md}]
+indent_style = unset
@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
@@ -1,20 +1,20 @@
-# y/nfcmggstructural: Contributing Guidelines
+# nf-cmgg/structural: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving y/nfcmggstructural.
+Many thanks for taking an interest in improving nf-cmgg/structural.
 
-We try to manage the required tasks for y/nfcmggstructural using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-cmgg/structural 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 y/nfcmggstructural, the standard workflow is as follows:
+If you'd like to write some code for nf-cmgg/structural, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [y/nfcmggstructural issues](https://github.com/y/nfcmggstructural/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 [y/nfcmggstructural repository](https://github.com/y/nfcmggstructural) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-cmgg/structural issues](https://github.com/nf-cmgg/structural/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 [nf-cmgg/structural repository](https://github.com/nf-cmgg/structural) 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
@@ -23,6 +23,12 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## 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.
 
@@ -50,9 +56,13 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
+## Getting help
+
+For further information/help, please consult the [nf-core/structural documentation](https://nf-co.re/structural/usage) and don't hesitate to get in touch on the nf-core Slack [#structural](https://nfcore.slack.com/channels/structural) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
 ## Pipeline contribution conventions
 
-To make the y/nfcmggstructural 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.
+To make the nf-cmgg/structural 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
 
@@ -79,7 +89,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 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 `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+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
 
@@ -95,3 +105,18 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### 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/nf-cmgg/structural/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
@@ -1,53 +1,56 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+labels: [bug]
 body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/structural pipeline documentation](https://nf-co.re/structural/usage)
+
   - 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.
+      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 ...
-
+      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.
+      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. 21.10.3)_
+      description: "* Nextflow version _(eg. 23.10.0)_
 
         * Hardware _(eg. HPC, Desktop, Cloud)_
-
         * Executor _(eg. slurm, local, awsbatch)_
 
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-        * Version of y/nfcmggstructural _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-cmgg/structural _(eg. 1.1, 1.5, 1.8.2)_
 
         "
@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #structural channel"
+    url: https://nfcore.slack.com/channels/structural
+    about: Discussion about the nf-core/structural pipeline
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the y/nfcmggstructural pipeline
+description: Suggest an idea for the nf-cmgg/structural pipeline
 labels: enhancement
 body:
   - type: textarea
 
@@ -1,24 +1,26 @@
 <!--
-# y/nfcmggstructural pull request
+# nf-cmgg/structural pull request
 
-Many thanks for contributing to y/nfcmggstructural!
+Many thanks for contributing to nf-cmgg/structural!
 
 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/y/nfcmggstructural/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/structural/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/y/nfcmggstructural/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/structural/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>`).
+- [ ] Ensure the test suite passes (`nf-test test`).
+- [ ] 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.
+- [ ] Parameters Documentation is updated with `nf-core schema docs --format markdown --output docs/parameters.md --force`
 - [ ] `CHANGELOG.md` is updated.
 - [ ] `README.md` is updated (including new tool citations and authors/contributors).
@@ -11,15 +11,15 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'y/nfcmggstructural'
+        if: github.repository == 'nf-cmgg/structural'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == y/nfcmggstructural ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/structural ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
 
@@ -0,0 +1,38 @@
+name: build docs
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - name: Obtain version from MANIFEST.MF
+        run: echo "pipeline_version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)" >> $GITHUB_ENV
+      - name: Setup git user
+        run: |
+          git config --global user.name "${{github.actor}}"
+          git config --global user.email "${{github.actor}}@users.noreply.github.com"
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - name: Install dependencies
+        run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
+      - name: Build docs
+        run: mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+      - name: Set default docs
+        run: mike set-default --push latest