Dev -> Master for v2.11

.github/CONTRIBUTING.md

@@ -92,7 +92,7 @@ pre-commit run --all
 ## API Documentation
 
 We aim to write function docstrings according to the [Google Python style-guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings). These are used to automatically generate package documentation on the nf-core website using Sphinx.
-You can find this documentation here: [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
+You can find this documentation here: [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/)
 
 If you would like to test the documentation, you can install Sphinx locally by following Sphinx's [installation instruction](https://www.sphinx-doc.org/en/master/usage/installation.html).
 Once done, you can run `make clean` and then `make html` in the `docs/api` directory of `nf-core tools`.

.github/renovate.json5

@@ -0,0 +1,5 @@
+{
+    $schema: "https://docs.renovatebot.com/renovate-schema.json",
+    extends: ["github>nf-core/ops//.github/renovate/default.json5"],
+    baseBranches: ["dev"],
+}

.github/workflows/create-lint-wf.yml

@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -27,7 +27,7 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
@@ -48,84 +48,101 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+      - name: Install Prettier and editorconfig-checker
+        run: npm install -g prettier editorconfig-checker
 
       # Build a pipeline from the template
       - name: nf-core create
-        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        run: |
+          mkdir create-lint-wf && cd create-lint-wf
+          export NXF_WORK=$(pwd)
+          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
 
       # Try syncing it before we change anything
       - name: nf-core sync
         run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       # Build a module from the template
       - name: nf-core modules create
         run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
+        working-directory: create-lint-wf
 
       # Run code style linting
       - name: Run Prettier --check
-        run: prettier --check nf-core-testpipeline
+        run: prettier --check create-lint-wf/nf-core-testpipeline
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        working-directory: create-lint-wf
 
       # Update modules to the latest version
       - name: nf-core modules update
         run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+        working-directory: create-lint-wf
 
       # Remove TODO statements
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+        working-directory: create-lint-wf
 
       # Replace zenodo.XXXXXX to pass readme linting
       - name: replace zenodo.XXXXXX
         run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+        working-directory: create-lint-wf
 
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+        working-directory: create-lint-wf
 
       # Run the other nf-core commands
       - name: nf-core list
         run: nf-core --log-file log.txt list
+        working-directory: create-lint-wf
 
       # - name: nf-core licences
       #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
       - name: nf-core schema
         run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
+        working-directory: create-lint-wf
 
       - name: nf-core bump-version
         run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
+        working-directory: create-lint-wf
 
       - name: nf-core lint in release mode
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+        working-directory: create-lint-wf
 
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
+        working-directory: create-lint-wf
 
       - name: nf-core modules install gitlab
         run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       - name: nf-core modules list local
         run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       - name: nf-core modules list remote
         run: nf-core --log-file log.txt modules list remote
+        working-directory: create-lint-wf
 
       - name: nf-core modules list remote gitlab
         run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+        working-directory: create-lint-wf
 
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: log.txt
+          path: create-lint-wf/log.txt

.github/workflows/create-test-lint-wf-template.yml

@@ -16,6 +16,7 @@ concurrency:
 
 env:
   NXF_ANSI_LOG: false
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   RunTestWorkflow:
@@ -32,7 +33,7 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
@@ -51,7 +52,9 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -63,75 +66,86 @@ jobs:
       # Create template files
       - name: Create template skip all (except github)
         run: |
-          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > template_skip_all.yml
+          mkdir create-test-lint-wf
+          export NXF_WORK=$(pwd)
+          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
 
       - name: Create template skip github_badges
         run: |
-          printf "prefix: my-prefix\nskip: github_badges" > template_skip_github_badges.yml
+          printf "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
 
       - name: Create template skip igenomes
         run: |
-          printf "prefix: my-prefix\nskip: igenomes" > template_skip_igenomes.yml
+          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
 
       - name: Create template skip ci
         run: |
-          printf "prefix: my-prefix\nskip: ci" > template_skip_ci.yml
+          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
 
       - name: Create template skip nf_core_configs
         run: |
-          printf "prefix: my-prefix\nskip: nf_core_configs" > template_skip_nf_core_configs.yml
+          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
+          cd create-test-lint-wf
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |
+          cd create-test-lint-wf
           nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder
         run: |
-          rm -rf ./results
+          rm -rf create-test-lint-wf/results
 
       # Try syncing it before we change anything
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/
+        run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
       - name: Run Prettier --check
-        run: prettier --check my-prefix-testpipeline
+        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        working-directory: create-test-lint-wf
 
       # Remove TODO statements
       - name: remove TODO
         run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+        working-directory: create-test-lint-wf
 
       # Replace zenodo.XXXXXX to pass readme linting
       - name: replace zenodo.XXXXXX
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+        working-directory: create-test-lint-wf
 
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned
+        working-directory: create-test-lint-wf
 
       # Run bump-version
       - name: nf-core bump-version
         run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1
+        working-directory: create-test-lint-wf
 
       # Run nf-core linting in release mode
       - name: nf-core lint in release mode
         run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release
+        working-directory: create-test-lint-wf
 
       - name: Tar files
         run: tar -cvf artifact_files.tar log.txt template_skip*.yml
+        working-directory: create-test-lint-wf
 
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: artifact_files.tar
+          path: create-test-lint-wf/artifact_files.tar

.github/workflows/create-test-wf.yml

@@ -26,7 +26,7 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11
@@ -46,6 +46,8 @@ jobs:
 
       - name: Run nf-core/tools
         run: |
+          mkdir create-test-wf && cd create-test-wf
+          export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
           nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
@@ -54,4 +56,4 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: log.txt
+          path: create-test-wf/log.txt

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.11

.github/workflows/fix-linting.yml

@@ -13,7 +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@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php