Fix linting part 1

.editorconfig

@@ -13,3 +13,7 @@ indent_size = 2
 
 [*.nf.test]
 insert_final_newline = false
+
+# ignore Readme
+[README.md]
+indent_style = unset

.github/workflows/fix-linting.yml

@@ -1,5 +1,4 @@
-name: fix-linting
-run-name: fix linting (automated)
+name: Fix linting from a comment
 on:
   issue_comment:
     types: [created]
@@ -14,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,40 +31,56 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
+        with:
+          node-version: 20
+      - run: npm install --only=dev
+
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
-          else
-            echo "::set-output name=result::fail"
-          fi
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Post nothing-to-do comment
-        if: steps.prettier_status.outputs.result == 'pass'
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: ${{ steps.pre-commit.outcome }} == 'success'
         uses: peter-evans/create-or-update-comment@v3
         with:
-          issue-number: ${{ github.event.issue.number }}
-          body: |
-            Nothing for me to do here! :shrug:
-            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+          comment-id: ${{ github.event.comment.id }}
+          reactions: green_check_mark
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: ${{ steps.pre-commit.outcome }} == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'success'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: pencil2
+
+      - name: react if linting errors were not fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'failure'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: x
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.

.github/workflows/test.yml

@@ -23,46 +23,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - uses: actions/setup-python@v3
-      - uses: pre-commit/[email protected]
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c #v5
+      - name: Fetch master
+        run: |
+          git fetch --no-tags --prune --depth=1 origin +refs/heads/*:refs/remotes/origin/*
+
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507 # v3.0.0
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
         # easier to fix these as they come up rather than everything at once.
         with:
-          extra_args: ""
-
-  prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g [email protected]
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  editorconfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
-
+          extra_args: " --files $(git diff --name-only master...)"
   pytest-changes:
     name: pytest-changes
     runs-on: ubuntu-latest
@@ -96,9 +67,6 @@ jobs:
         id: get_tags
         run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
 
-      - name: debug
-        run: cat .github/tags.yml
-
       # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
       - uses: mirpedrol/paths-filter@main
         id: filter
@@ -107,7 +75,7 @@ jobs:
           token: ""
 
   nf-core-lint:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: nf-core-lint
     needs: [pytest-changes, nf-test-changes]
     if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }}
@@ -126,13 +94,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: "pip"
 
       - name: Install pip
         run: python -m pip install --upgrade pip
@@ -142,7 +104,7 @@ jobs:
           distribution: "temurin"
           java-version: "17"
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
 
       - name: Install nf-core tools development version
         run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
@@ -160,7 +122,7 @@ jobs:
         if: ${{ startsWith(matrix.tags, 'subworkflows/') }}
 
   pytest:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: pytest
     needs: [pytest-changes]
     if: needs.pytest-changes.outputs.modules != '[]'
@@ -374,6 +336,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
+          cache: "pip"
 
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
@@ -383,7 +346,7 @@ jobs:
           distribution: "temurin"
           java-version: "17"
       - name: Setup Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -401,6 +364,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: "latest"
+          auto-update-conda: true
           channels: conda-forge,bioconda,defaults
           python-version: ${{ matrix.python-version }}
 
@@ -459,7 +423,7 @@ jobs:
             !${{ github.workspace }}/.singularity
 
   nf-test:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: nf-test
     needs: [nf-test-changes]
     if: needs.nf-test-changes.outputs.modules != '[]'
@@ -578,20 +542,31 @@ jobs:
         with:
           distribution: "temurin"
           java-version: "17"
+
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
+
+      - name: Look if nf-test is already installed and write to env variable
+        id: check-nftest
+        run: |
+          if [ -f /usr/local/bin/nf-test ]; then
+            echo "nftest_installed=true" >> $GITHUB_ENV
+          else
+            echo "nftest_installed=false" >> $GITHUB_ENV
+          fi
 
       - name: Cache nf-test installation
+        if: env.nftest_installed != 'true'
         id: cache-software
         uses: actions/cache@v3
         with:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
+        if: steps.cache-software.outputs.cache-hit != 'true' && env.nftest_installed != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
@@ -606,6 +581,11 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
       - name: Set up miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -619,9 +599,9 @@ jobs:
           conda clean -a
           conda install -n base conda-libmamba-solver
           conda config --set solver libmamba
-          pip install pdiff
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
+          python -m pip install --upgrade pip pdiff
 
       # Set up secrets
       - name: Set up nextflow secrets
@@ -655,7 +635,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    needs: [pre-commit, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
     if: always()
     steps:
       - name: All tests ok

.pre-commit-config.yaml

@@ -3,18 +3,35 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+        exclude: ".*(test).*"
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.27.0
     hooks:
       - id: check-jsonschema
+        name: check meta.yml's of modules
         # match meta.ymls in one of the subdirectories of modules/nf-core
         files: ^modules/nf-core/.*/meta\.yml$
-        args: ["--schemafile", "modules/yaml-schema.json"]
+        args: ["--schemafile", "modules/meta-schema.json"]
+      - id: check-jsonschema
+        name: check environment.yml's of modules
+        # match environment.ymls in one of the subdirectories of modules/nf-core
+        files: ^modules/nf-core/.*/environment\.yml$
+        args: ["--schemafile", "modules/environment-schema.json"]
       - id: check-jsonschema
+        name: check meta.yml's of subworkflows
         # match meta.ymls in one of the subdirectories of subworkflows/nf-core
         files: ^subworkflows/nf-core/.*/meta\.yml$
-        args: ["--schemafile", "subworkflows/yaml-schema.json"]
-      - id: check-github-workflows
+        args: ["--schemafile", "subworkflows/meta-schema.json"]
+      - id: check-jsonschema
+        name: check environment.yml's of subworkflows
+        # match environment.ymls in one of the subdirectories of subworkflows/nf-core
+        files: ^subworkflows/nf-core/.*/environment\.yml$
+        args: ["--schemafile", "subworkflows/environment-schema.json"]
   - repo: https://github.com/renovatebot/pre-commit-hooks
     rev: 37.127.0
     hooks:

modules/nf-core/ampcombi/meta.yml

@@ -18,18 +18,18 @@ tools:
       homepage: "https://github.com/Darcy220606/AMPcombi"
       documentation: "https://github.com/Darcy220606/AMPcombi"
       tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - amp_input:
-      type: folder or filelist
+      type: directory
       description: The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.
   - faa_input:
-      type: folder or file
+      type: directory
       description: The path to the folder or file corresponding to the respective protein fasta files with '.faa' extension. Filenames have to contain the corresponding sample-name, i.e. sample_1.faa
       pattern: "*/"
   - amp_database:

modules/nf-core/angsd/docounts/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "http://www.popgen.dk/angsd/"
       tool_dev_url: "https://github.com/ANGSD/angsd"
       doi: "10.1186/s12859-014-0356-4"
-      licence: "['GPL v3, MIT']"
+      licence: ["GPL v3", "MIT"]
 input:
   - meta:
       type: map

modules/nf-core/annotsv/annotsv/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: "https://lbgi.fr/AnnotSV/"
       documentation: "https://lbgi.fr/AnnotSV/"
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
-      licence: "GPL-3.0"
+      licence: ["GPL-3.0"]
 input:
   - meta:
       type: map

modules/nf-core/annotsv/installannotations/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: "https://lbgi.fr/AnnotSV/"
       documentation: "https://lbgi.fr/AnnotSV/"
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 output:
   - versions:
       type: file