dev -> main for 4.0.2 (#4255)

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Author: mashehu

CHANGELOG.md

@@ -1,6 +1,17 @@
 # nf-core/tools: Changelog
 
-## v4.0.1
+## [v4.0.2 - Bold Boa Patch 2](https://github.com/nf-core/tools/releases/tag/4.0.2) - [2026-04-30]
+
+### General
+
+- add `pipeline_dir` to search directories for include statements ([#4252](https://github.com/nf-core/tools/pull/4252))
+
+### Template
+
+- fix version capture in downloads_action ([#4251](https://github.com/nf-core/tools/pull/4251))
+- Remove format constraint for igenomes_base ([#4253](https://github.com/nf-core/tools/pull/4253))
+
+## [v4.0.1 - Bold Boa Patch](https://github.com/nf-core/tools/releases/tag/4.0.1) - [2026-04-29]
 
 ### General
 
@@ -13,7 +24,7 @@
 
 - Allow task.ext.prefix2 in modules linting ([#4234](https://github.com/nf-core/tools/pull/4234))
 
-## [v4.0.0 - Bold Boa](https://github.com/nf-core/tools/releases/tag/4.0.0) - [2026-04-27]
+## [v4.0.0 - Bold Boa](https://github.com/nf-core/tools/releases/tag/4.0.0) - [2026-04-28]
 
 ### General
 

Dockerfile

@@ -22,7 +22,7 @@ RUN mkdir -p /usr/share/man/man1 \
 
 # Setup ARG for NXF_VER ENV
 ARG NXF_VER=""
-ENV NXF_VER ${NXF_VER}
+ENV NXF_VER=${NXF_VER}
 # Install Nextflow
 RUN curl -s https://get.nextflow.io | bash \
     && mv nextflow /usr/local/bin \

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -38,6 +38,9 @@ jobs:
     runs-on: ubuntu-latest
     needs: configure
     steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
@@ -55,10 +58,9 @@ jobs:
           apptainer-version: 1.3.4{% raw %}
 
       - name: Read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
-        with:
-          config: ${{ github.workspace }}/.nf-core.yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
 
       - name: Install dependencies
         run: |

nf_core/pipeline-template/nextflow_schema.json

@@ -77,7 +77,6 @@
                 },
                 "igenomes_base": {
                     "type": "string",
-                    "format": "directory-path",
                     "description": "The base path to the igenomes reference files",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,

nf_core/pipelines/containers_utils.py

@@ -57,35 +57,37 @@ def parse_module_paths(self) -> dict[str, Path]:
         # Captures the first name (original) and the path, ignoring any alias
         include_pattern = re.compile(r"include\s*\{\s*(\w+).*?\}\s*from\s+['\"]([^'\"]+)['\"]")
 
-        # Search in workflows, modules, and subworkflows directories
+        # Search in root (main.nf), workflows, modules, and subworkflows directories
         search_dirs = ["workflows", "modules", "subworkflows"]
 
+        nf_files_to_search = list(self.workflow_directory.glob("*.nf"))
         for search_dir in search_dirs:
             search_path = self.workflow_directory / search_dir
             if not search_path.exists():
                 continue
+            nf_files_to_search.extend(search_path.rglob("*.nf"))
 
-            for nf_file in search_path.rglob("*.nf"):
-                try:
-                    content = nf_file.read_text()
-                    for match in include_pattern.finditer(content):
-                        process_name = match.group(1)
-                        relative_path = match.group(2)
+        for nf_file in nf_files_to_search:
+            try:
+                content = nf_file.read_text()
+                for match in include_pattern.finditer(content):
+                    process_name = match.group(1)
+                    relative_path = match.group(2)
 
-                        # Only process paths that contain 'modules/'
-                        if "modules/" not in relative_path:
-                            continue
+                    # Only process paths that contain 'modules/'
+                    if "modules/" not in relative_path:
+                        continue
 
-                        # Extract everything from 'modules/' onwards, removing any '/main' suffix
-                        module_path_str = relative_path[relative_path.find("modules/") :]
-                        module_path_str = module_path_str.replace("/main", "")
+                    # Extract everything from 'modules/' onwards, removing any '/main' suffix
+                    module_path_str = relative_path[relative_path.find("modules/") :]
+                    module_path_str = module_path_str.replace("/main", "")
 
-                        module_paths[process_name] = Path(module_path_str)
-                        log.debug(f"Found include: {process_name} -> {module_path_str}")
+                    module_paths[process_name] = Path(module_path_str)
+                    log.debug(f"Found include: {process_name} -> {module_path_str}")
 
-                except OSError as e:
-                    log.debug(f"Error parsing {nf_file}: {e}")
-                    continue
+            except OSError as e:
+                log.debug(f"Error parsing {nf_file}: {e}")
+                continue
 
         return module_paths
 
@@ -162,7 +164,7 @@ def generate_container_configs(
                     has_warnings = True
                     continue
         if has_warnings:
-            log.info(
+            log.debug(
                 "Generated container configs for the pipeline. Not all containers were found. Run with `-v` to see detailed warning messages."
             )
         else:

pyproject.toml

@@ -11,7 +11,7 @@ nf_core = ["**/*"]
 
 [project]
 name = "nf-core"
-version = "4.0.1"
+version = "4.0.2"
 description = "Helper tools for use with nf-core Nextflow pipelines."
 readme = "README.md"
 license = "MIT"