Merge branch 'master' into modules/regenie-runl0-create

Author: lyh970817

.github/workflows/clean-up.yml

@@ -11,7 +11,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an @nf-core/modules 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/modules contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/close-wishlist.yml

@@ -10,7 +10,7 @@ jobs:
     permissions:
       issues: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # v10
         with:
           stale-issue-message: "This issue has been tagged as wishlist and no one has assigned themselves to it within a year. It will be closed in 10 days unless someone assigns themselves to it."
           close-issue-message: "This issue was closed because it has been tagged as wishlist and no one worked on it for over a year."

.github/workflows/fix-linting.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
         continue-on-error: true
 
       # indication that the linting has finished

.github/workflows/lint.yml

@@ -39,9 +39,9 @@ jobs:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
       - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3
+        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
         with:
-          extra_args: ""
+          extra-args: ""
 
   ###################
   # nf-core linting #

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

@@ -104,7 +104,11 @@ jobs:
   # Standard GPU tests (g4dn.xlarge - 4 vCPU, 16 GB RAM, T4 GPU)
   # Runs tests tagged "gpu" (20+ modules: parabricks, amulety, cellpose, etc.)
   nf-test-gpu:
-    runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64"
+    runs-on:
+      - runs-on=${{ github.run_id }}
+      - family=g4dn.xlarge
+      - image=ubuntu24-gpu-x64
+      - volume=40gb
     name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }}

.github/workflows/nf-test.yml

@@ -93,6 +93,7 @@ jobs:
       - runs-on=${{ github.run_id }}
       - runner=4cpu-linux-${{ matrix.arch }}
       - image=ubuntu24-full-${{ matrix.arch }}
+      - volume=40gb
     name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}

.github/workflows/reminder.yml

@@ -10,7 +10,7 @@ jobs:
     permissions:
       issues: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@eb5cf3af3ac0a1aa4c9c45633dd1ae542a27a899 # v10
         with:
           stale-issue-message: "This is a reminder that you assigned yourself to this issue to create a new module / new subworkflow. Please remove yourself from the Assignees if you do not plan to work on this anymore."
           days-before-stale: 178

.pre-commit-config.yaml

@@ -3,6 +3,7 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        priority: 0
         entry: prettier --experimental-cli --write --ignore-unknown --no-cache
         exclude: |
           (?x)^(
@@ -15,12 +16,14 @@ repos:
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
+        priority: 10
         args: [--markdown-linebreak-ext=md]
         exclude: |
           (?x)^(
               .*\.snap$
           )$
       - id: end-of-file-fixer
+        priority: 10
         exclude: |
           (?x)^(
               .*\.snap$
@@ -30,41 +33,49 @@ repos:
     rev: 0.37.2
     hooks:
       - id: check-jsonschema
+        priority: 20
         name: "Match meta.ymls in one of the subdirectories of modules/nf-core"
         files: ^modules/nf-core/.*/meta\.yml$
         types: [yaml]
         args: ["--schemafile", "modules/yaml-schema.json"]
       - id: check-jsonschema
+        priority: 20
         name: "Validate environment.ymls against schema"
         files: ^modules/nf-core/.*/environment\.yml$
         types: [yaml]
         args: ["--schemafile", "modules/environment-schema.json"]
       - id: check-jsonschema
+        priority: 20
         name: "Match meta.ymls in one of the subdirectories of subworkflows/nf-core"
         files: ^subworkflows/nf-core/.*/meta\.yml$
         types: [yaml]
         args: ["--schemafile", "subworkflows/yaml-schema.json"]
       - id: check-github-workflows
+        priority: 20
 
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.13
     hooks:
-      - id: ruff
+      - id: ruff-check
+        priority: 10
         files: \.py$
         args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
       - id: ruff-format # formatter
-    # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
+        priority: 0
+  # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
     rev: v2.14.0
     hooks:
       - id: hadolint-docker
+        priority: 0
         args: ["--failure-threshold", "error"]
 
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit
     rev: v0.3.0
     hooks:
       - id: nextflow-lint
+        priority: 0
         files: '\.nf$|nextflow\.config$'
         args: ["-output", "json"]
         # TODO add formatting at a later stage

modules/environment-schema.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "conda environment yaml",
     "description": "Validate the environment.yml file for an nf-core module",
     "type": "object",

modules/meta-schema.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "Meta yaml",
     "description": "Validate the meta yaml file for an nf-core module",
     "type": "object",
@@ -12,6 +12,10 @@
             "type": "string",
             "description": "Description of the module"
         },
+        "deprecated": {
+            "type": "boolean",
+            "description": "Whether the module is deprecated and should not be used in new pipelines"
+        },
         "keywords": {
             "type": "array",
             "description": "Keywords for the module",
@@ -53,14 +57,13 @@
                                 "pattern": "^https?://.*$"
                             },
                             "doi": {
+                                "type": "string",
                                 "description": "DOI of the tool",
                                 "anyOf": [
                                     {
-                                        "type": "string",
                                         "pattern": "^10\\.\\d{4,9}\\/[^,]+$"
                                     },
                                     {
-                                        "type": "string",
                                         "enum": ["no DOI available"]
                                     }
                                 ]
@@ -114,39 +117,16 @@
             }
         },
         "input": {
-            "type": "array",
-            "description": "Input channels for the module",
-            "items": {
-                "oneOf": [
-                    {
-                        "$ref": "#/definitions/channelElement"
-                    },
-                    {
-                        "type": "array",
-                        "items": {
-                            "$ref": "#/definitions/channelElement"
-                        }
-                    }
-                ]
-            }
+            "$ref": "#/$defs/channelArray",
+            "description": "Input channels for the module"
         },
         "output": {
-            "type": "object",
-            "description": "Output channels for the module",
-            "patternProperties": {
-                ".*": {
-                    "$ref": "#/definitions/channelArray"
-                }
-            }
+            "$ref": "#/$defs/channelMap",
+            "description": "Output channels for the module"
         },
         "topics": {
-            "type": "object",
-            "description": "Topics of the module",
-            "patternProperties": {
-                ".*": {
-                    "$ref": "#/definitions/channelArray"
-                }
-            }
+            "$ref": "#/$defs/channelMap",
+            "description": "Topics of the module"
         },
         "authors": {
             "type": "array",
@@ -170,44 +150,55 @@
                     "type": "object",
                     "description": "Docker containers for different architectures",
                     "additionalProperties": {
-                        "$ref": "#/definitions/container"
+                        "$ref": "#/$defs/container"
                     }
                 },
                 "singularity": {
                     "type": "object",
                     "description": "Singularity containers for different architectures",
                     "additionalProperties": {
-                        "allOf": [
-                            {
-                                "$ref": "#/definitions/container"
-                            },
-                            {
-                                "properties": {
-                                    "name": {
-                                        "pattern": "^oras://.*$"
-                                    }
-                                },
-                                "required": ["https"]
+                        "$ref": "#/$defs/container",
+                        "properties": {
+                            "name": {
+                                "pattern": "^oras://.*$"
                             }
-                        ]
+                        },
+                        "required": ["https"]
                     }
                 },
                 "conda": {
                     "type": "object",
                     "description": "Conda lock files for different architectures",
                     "additionalProperties": {
-                        "$ref": "#/definitions/condaLockFile"
+                        "type": "object",
+                        "description": "Conda lock file information",
+                        "properties": {
+                            "lock_file": {
+                                "type": "string",
+                                "description": "Path to the conda lock file, relative to the repository root",
+                                "pattern": "^.*\\.conda-lock/.*\\.txt$"
+                            }
+                        },
+                        "required": ["lock_file"]
                     }
                 }
             }
         }
     },
-    "definitions": {
+    "$defs": {
+        "channelMap": {
+            "type": "object",
+            "patternProperties": {
+                ".*": {
+                    "$ref": "#/$defs/channelArray"
+                }
+            }
+        },
         "channelElement": {
             "type": "object",
             "patternProperties": {
                 ".*": {
-                    "$ref": "#/definitions/elementProperties"
+                    "$ref": "#/$defs/elementProperties"
                 }
             }
         },
@@ -216,12 +207,12 @@
             "items": {
                 "oneOf": [
                     {
-                        "$ref": "#/definitions/channelElement"
+                        "$ref": "#/$defs/channelElement"
                     },
                     {
                         "type": "array",
                         "items": {
-                            "$ref": "#/definitions/channelElement"
+                            "$ref": "#/$defs/channelElement"
                         }
                     }
                 ]
@@ -291,18 +282,6 @@
                 }
             },
             "required": ["name", "build_id"]
-        },
-        "condaLockFile": {
-            "type": "object",
-            "description": "Conda lock file information",
-            "properties": {
-                "lock_file": {
-                    "type": "string",
-                    "description": "Path to the conda lock file, relative to the repository root",
-                    "pattern": "^.*\\.conda-lock/.*\\.txt$"
-                }
-            },
-            "required": ["lock_file"]
         }
     },
     "required": ["name", "description", "keywords", "authors", "output", "tools"]