changed locidex report default parameter

.editorconfig

@@ -8,8 +8,8 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
-indent_size = 2
+[*.{json,md,yml,yaml,html,css,scss,js,cff}]
+indent_size = unset
 
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
@@ -22,3 +22,4 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# mk-kondo/mikrokondo: Contributing Guidelines
+# phac-nml/mikrokondo: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving mk-kondo/mikrokondo.
+Many thanks for taking an interest in improving phac-nml/mikrokondo.
 
-We try to manage the required tasks for mk-kondo/mikrokondo using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for phac-nml/mikrokondo 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 mk-kondo/mikrokondo, the standard workflow is as follows:
+If you'd like to write some code for phac-nml/mikrokondo, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [mk-kondo/mikrokondo issues](https://github.com/mk-kondo/mikrokondo/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 [mk-kondo/mikrokondo repository](https://github.com/mk-kondo/mikrokondo) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [phac-nml/mikrokondo issues](https://github.com/phac-nml/mikrokondo/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 [phac-nml/mikrokondo repository](https://github.com/phac-nml/mikrokondo) 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
@@ -52,7 +52,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the mk-kondo/mikrokondo 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 phac-nml/mikrokondo 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
 
@@ -102,7 +102,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/mk-kondo/mikrokondo/codespaces)
+- Open the repo in [Codespaces](https://github.com/phac-nml/mikrokondo/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,52 +2,52 @@ 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. 22.10.1)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of mk-kondo/mikrokondo _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - 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. 22.10.1)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of mk-kondo/mikrokondo _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/mk-kondo/mik
 
 - [ ] 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/mk-kondo/mikrokondo/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/phac-nml/mikrokondo/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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/ci.yml

@@ -60,4 +60,3 @@ jobs:
       - name: Nextflow run with test profile
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-

.github/workflows/linting.yml

@@ -1,7 +1,7 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
-# that the code meets the nf-core guidelines.
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines. {%- raw %}
 on:
   push:
     branches:
@@ -14,41 +14,54 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
 
       - name: Run pre-commit
-        #run: pre-commit run --all-files
-        run: pre-commit run --files nf-test.config
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -61,10 +74,10 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
             lint_log.txt
             lint_results.md
-            PR_number.txt
+            PR_number.txt {%- endraw %}

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/spellcheck.yml

@@ -1,4 +1,3 @@
-
 name: Spellcheck Action
 
 on:
@@ -12,20 +11,19 @@ jobs:
     name: Spellcheck
     runs-on: ubuntu-latest
     steps:
+      # The checkout step
+      - uses: actions/checkout@v4
 
-    # The checkout step
-    - uses: actions/checkout@v4
-
-    - uses: rojopolis/spellcheck-github-actions@v0
-      name: Spellcheck
-      with:
-        source_files: README.md CHANGELOG.md nextflow_schema.json assets/schema_input.json
-        task_name: Markdown
-        output_file: spellcheck-output.txt
+      - uses: rojopolis/spellcheck-github-actions@v0
+        name: Spellcheck
+        with:
+          source_files: README.md CHANGELOG.md nextflow_schema.json assets/schema_input.json
+          task_name: Markdown
+          output_file: spellcheck-output.txt
 
-    - uses: actions/upload-artifact@v4
-      if: '!cancelled()'
-      name: Archive spellcheck output
-      with:
-        name: Spellcheck artifact
-        path: spellcheck-output.txt
+      - uses: actions/upload-artifact@v4
+        if: "!cancelled()"
+        name: Archive spellcheck output
+        with:
+          name: Spellcheck artifact
+          path: spellcheck-output.txt

.gitlab-ci.yml

@@ -8,4 +8,4 @@ pages:
     paths:
       - public
   rules:
-    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: "$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH"

.nf-core.yml

@@ -1,5 +1,5 @@
 repository_type: pipeline
-nf_core_version: "3.0.2"
+nf_core_version: "3.1.1"
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md

.pre-commit-config.yaml

@@ -3,8 +3,10 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        exclude: ^(tests/|utils/|docs/)
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
+        exclude: ^(tests/|utils/|docs/)

.spellcheck.yaml

@@ -1,23 +1,23 @@
 matrix:
-- name: Markdown
-  sources:
-  - '!venv/**/*.md|**/*.md'
-  default_encoding: utf-8
-  aspell:
-    lang: en
-    ignore-case: true
-  dictionary:
-    encoding: utf-8
-    wordlists:
-    - .wordlist.txt
-  pipeline:
-  - pyspelling.filters.markdown:
-      markdown_extensions:
-      - pymdownx.superfences
-      - pymdownx.striphtml
-  - pyspelling.filters.html:
-      comments: false
-      ignores:
-      - code
-      - pre
-      - small
+  - name: Markdown
+    sources:
+      - "!venv/**/*.md|**/*.md"
+    default_encoding: utf-8
+    aspell:
+      lang: en
+      ignore-case: true
+    dictionary:
+      encoding: utf-8
+      wordlists:
+        - .wordlist.txt
+    pipeline:
+      - pyspelling.filters.markdown:
+          markdown_extensions:
+            - pymdownx.superfences
+            - pymdownx.striphtml
+      - pyspelling.filters.html:
+          comments: false
+          ignores:
+            - code
+            - pre
+            - small