Merge dev to master

.devcontainer/devcontainer.json

@@ -10,15 +10,7 @@
         "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"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.editorconfig

@@ -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

.github/CONTRIBUTING.md

@@ -1,24 +1,22 @@
-# tomte: Contributing Guidelines
+# genomic-medicine-sweden/tomte: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving tomte.
+Many thanks for taking an interest in improving genomic-medicine-sweden/tomte.
 
-We try to manage the required tasks for tomte using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for genomic-medicine-sweden/tomte 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 ;)
 
-:::info
 If you need help using or modifying genomic-medicine-sweden/tomte then the best place to ask is by creating an [issue] (https://github.com/genomic-medicine-sweden/tomte/issues).
-:::
 
 ## Contribution workflow
 
-If you'd like to write some code for tomte, the standard workflow is as follows:
+If you'd like to write some code for genomic-medicine-sweden/tomte, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [tomte issues](https://github.com/genomic-medicine-sweden/tomte/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 [tomte repository](https://github.com/genomic-medicine-sweden/tomte) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/tomte issues](https://github.com/genomic-medicine-sweden/tomte/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 [genomic-medicine-sweden/tomte repository](https://github.com/genomic-medicine-sweden/tomte) 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
@@ -27,6 +25,12 @@ 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.
 
@@ -60,7 +64,7 @@ For further information/help, please consult the [tomte documentation](https://g
 
 ## Pipeline contribution conventions
 
-To make the tomte 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 genomic-medicine-sweden/tomte 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
 
@@ -87,7 +91,7 @@ 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
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,49 +2,52 @@ name: Bug report
 description: Report something that is broken or incorrect
 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)
-        - [tomte pipeline documentation](https://github.com/genomic-medicine-sweden/tomte)
-
   - 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. 23.04.0)_
+      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)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of tomte _(eg. 1.1, 1.5, 1.8.2)_
+
+        * Version of genomic-medicine-sweden/tomte _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/tomte pipeline
+description: Suggest an idea for the genomic-medicine-sweden/tomte pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!--
-# tomte pull request
+# genomic-medicine-sweden/tomte pull request
 
-Many thanks for contributing to tomte!
+Many thanks for contributing to genomic-medicine-sweden/tomte!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
@@ -18,6 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/tomte/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.

.github/workflows/branch.yml

@@ -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 == 'nf-core/tomte'
+        if: github.repository == 'genomic-medicine-sweden/tomte'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/tomte ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/tomte ]] && [[ $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:

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/tomte') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/tomte') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -28,13 +28,16 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."