Merge branch 'master' into assemblyscan_1.0.0

Author: eit-maxlcummins

.devcontainer/devcontainer.json

@@ -1,28 +1,20 @@
 {
-    "name": "nfcore",
-    "image": "nfcore/gitpod:dev",
-    "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",
-                "python.linting.enabled": true
-            },
+    "name": "nfcore-modules",
+    "image": "nfcore/devcontainer:dev",
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
     },
-    "features": {
-        "ghcr.io/devcontainers/features/github-cli:1.0.11": {
-            "digest": "sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312"
-        },
-        "ghcr.io/devcontainers/features/docker-in-docker:2.9.2": {
-            "digest": "sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf"
-        }
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "remoteUser": "root",
+    "privileged": true,
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Install prek hooks
+pip install prek
+prek install --install-hooks
+
+# Update welcome message
+echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/actions/nf-test-action/action.yml

@@ -28,7 +28,7 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
       with:
         python-version: "3.14"
 

.github/renovate.json5

@@ -2,14 +2,25 @@
     $schema: "https://docs.renovatebot.com/renovate-schema.json",
     extends: [
         "github>nf-core/ops//.github/renovate/default.json5",
-        "github>nf-core/ops//.github/renovate/process_updaters.json5",
+        // "github>nf-core/ops//.github/renovate/process_updaters.json5",
     ],
     prHeader: "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
     packageRules: [
         {
             matchDatasources: ["conda", "pypi", "docker"],
             automerge: false,
         },
+        {
+            matchManagers: [
+                "github-actions",
+                "npm",
+                "pip_requirements",
+                "pip_setup",
+            ],
+            groupName: "Infrastructural dependencies",
+            schedule: ["before 6am on Monday"],
+            matchPackageNames: ["!/biocontainers/*/"],
+        },
     ],
     customManagers: [
         {

.github/skip_nf_test.json

@@ -2,7 +2,6 @@
     "conda": [
         "modules/nf-core/angsd/gl",
         "modules/nf-core/annotsv/installannotations",
-        "modules/nf-core/backsub",
         "modules/nf-core/bakta/bakta",
         "modules/nf-core/bakta/baktadbdownload",
         "modules/nf-core/bases2fastq",

.github/workflows/fix-linting.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,26 +32,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      # 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 prek
+        id: prek
+        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1
+        continue-on-error: true
 
       - name: Post nothing-to-do comment
-        if: steps.prettier_status.outputs.result == 'pass'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
@@ -60,7 +47,7 @@ jobs:
             This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"

.github/workflows/lint.yml

@@ -35,11 +35,9 @@ jobs:
   pre-commit:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
-        with:
-          extra_args: ""
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - name: Run prek
+        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1
 
   ###################
   # nf-core linting #
@@ -64,7 +62,7 @@ jobs:
           sudo rm -rf ./* || true
           sudo rm -rf ./.* || true
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
@@ -85,10 +83,10 @@ jobs:
         with:
           script: |
             return [...new Set(${{ steps.filter.outputs.modules_files }}
-              .filter(x => x.endsWith('main.nf'))
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
               .map(path => path
                 .replace('modules/nf-core/', '')
-                .replace(/\/main\.nf$/, '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
               )
             )];
       - name: Get subworkflow name
@@ -97,10 +95,10 @@ jobs:
         with:
           script: |
             return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
-              .filter(x => x.endsWith('main.nf'))
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
               .map(path => path
                 .replace('subworkflows/nf-core/', '')
-                .replace(/\/main\.nf$/, '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
               )
             )];
 
@@ -128,9 +126,9 @@ jobs:
         run: |
           sudo rm -rf ./* || true
           sudo rm -rf ./.* || true
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
       - name: Set up Python
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
         with:
           python-version: "3.14"
 
@@ -176,9 +174,9 @@ jobs:
         run: |
           sudo rm -rf ./* || true
           sudo rm -rf ./.* || true
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
       - name: Set up Python
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
         with:
           python-version: "3.14"
 

.github/workflows/nf-test-gpu.yml

@@ -53,7 +53,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
 
@@ -105,7 +105,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
       - name: test cuda

.github/workflows/nf-test.yml

@@ -51,7 +51,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
 
@@ -112,7 +112,7 @@ jobs:
       filtered_paths: ${{ steps.filter.outputs.filtered_paths }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
 

.github/workflows/pytest-workflow.yml

@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "24.10.9"
 
 jobs:
   pytest-changes:
@@ -43,7 +43,7 @@ jobs:
       modules: ${{ steps.tags.outputs.modules }}
       subworkflows: ${{ steps.tags.outputs.subworkflows }}
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
@@ -76,8 +76,6 @@ jobs:
         profile: [conda, docker, singularity]
         exclude:
           - tags: nf-test
-          - profile: conda
-            tags: backsub
           - profile: conda
             tags: bases2fastq
           - profile: singularity
@@ -231,10 +229,10 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Set up Python
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
         with:
           python-version: "3.14"