nf-core · MatthiasZepper · Apr 3, 2025 · Mar 14, 2025 · Mar 14, 2025 · Mar 14, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Add Bluesky badge to readme ([#3475](https://github.com/nf-core/tools/pull/3475))
 - Run awsfulltest after release, and with dev revision on PRs to master ([#3485](https://github.com/nf-core/tools/pull/3485))
 - Add .nftignore to trigger list ([#3508](https://github.com/nf-core/tools/pull/3508))
+- Include the centralized nf-core configs also in offline mode, if a local copy is available. ([#3491](https://github.com/nf-core/tools/pull/3491))
 
 ### Linting
 
@@ -18,6 +19,7 @@
 - Fix: linting with comments after the input directive ([#3458](https://github.com/nf-core/tools/pull/3458))
 - EDAM ontology fixes ([#3460](https://github.com/nf-core/tools/pull/3460))
 - Fix default linting of nf-core components when `nf-core pipelines lint` is ran ([#3480](https://github.com/nf-core/tools/pull/3480))
+- Adapt the linter to the new notation used to include the centralized nf-core configs ([#3491](https://github.com/nf-core/tools/pull/3491))
 
 ### Modules
 

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -204,12 +204,16 @@ profiles {
 }
 
 {% if nf_core_configs -%}
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load {{ name }} custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
 
 // Load {{ name }} custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
+// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
 {%- endif %}
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile

diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py
@@ -21,12 +21,12 @@ def included_configs(self):
     with open(config_file) as fh:
         config = fh.read()
         if (
-            f"// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\""
+            f"// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\""
             in config
         ):
             failed.append("Pipeline config does not include custom configs. Please uncomment the includeConfig line.")
         elif (
-            f"includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\""
+            f"includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\""
             in config
         ):
             passed.append("Pipeline config includes custom configs.")

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
@@ -346,48 +346,41 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`")
 
         # Check that lines for loading custom profiles exist
-        old_lines = [
-            r"// Load nf-core custom profiles from different Institutions",
-            r"try {",
-            r'includeConfig "${params.custom_config_base}/nfcore_custom.config"',
-            r"} catch (Exception e) {",
-            r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")',
-            r"}",
-        ]
-        lines = [
-            r"// Load nf-core custom profiles from different Institutions",
-            r'''includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"''',
-        ]
+        old_institutional_config_pattern_1 = r"""try\s*{
+\s*includeConfig \"\${params\.custom_config_base}/nfcore_custom\.config\"
+\s*}\s*catch\s*\(Exception\s+e\)\s*{
+\s*System\.err\.println\(\"WARNING: Could not load nf-core/config profiles: \${params\.custom_config_base}/nfcore_custom\.config\"\)
+\s*}"""
+
+        old_institutional_config_pattern_2 = r"""includeConfig !System\.getenv\('NXF_OFFLINE'\) && params\.custom_config_base \? \"\${params\.custom_config_base}/nfcore_custom\.config\" : \"/dev/null\""""
+
+        current_institutional_config_pattern = r"""includeConfig params\.custom_config_base && \(!System\.getenv\('NXF_OFFLINE'\) \|\| !params\.custom_config_base\.startsWith\('http'\)\) \? \"\${params\.custom_config_base}/nfcore_custom\.config\" : \"/dev/null\""""
+
         path = Path(self.wf_path, "nextflow.config")
-        i = 0
         with open(path) as f:
-            for line in f:
-                if old_lines[i] in line:
-                    i += 1
-                    if i == len(old_lines):
-                        break
-                elif lines[i] in line:
-                    i += 1
-                    if i == len(lines):
-                        break
-                else:
-                    i = 0
-        if i == len(lines):
-            passed.append("Lines for loading custom profiles found")
-        elif i == len(old_lines):
-            failed.append(
-                "Old lines for loading custom profiles found. File should contain: ```groovy\n{}".format(
-                    "\n".join(lines)
+            content = f.read()
+
+            current_institutional_config_lines = [
+                "// Load nf-core custom profiles from different institutions",
+                """includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? \"${params.custom_config_base}/nfcore_custom.config" : "/dev/null\"""",
+            ]
+
+            if re.search(current_institutional_config_pattern, content, re.MULTILINE):
+                passed.append("Lines for loading custom profiles found")
+            elif re.search(old_institutional_config_pattern_1, content, re.MULTILINE) or re.search(
+                old_institutional_config_pattern_2, content, re.MULTILINE
+            ):
+                failed.append(
+                    "Outdated lines for loading custom profiles found. File should contain:\n```groovy\n{}\n```".format(
+                        "\n".join(current_institutional_config_lines)
+                    )
                 )
-            )
-        else:
-            lines[2] = f"\t{lines[2]}"
-            lines[4] = f"\t{lines[4]}"
-            failed.append(
-                "Lines for loading custom profiles not found. File should contain: ```groovy\n{}".format(
-                    "\n".join(lines)
+            else:
+                failed.append(
+                    "Lines for loading custom profiles not found. File should contain:\n```groovy\n{}\n```".format(
+                        "\n".join(current_institutional_config_lines)
+                    )
                 )
-            )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
     with open(Path(self.wf_path, "nextflow.config")) as f: