Template: remove try-catch blocks from nextflow.config

CHANGELOG.md

@@ -40,6 +40,7 @@
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
 - Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176))
+- Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167))
 
 ### Linting
 

nf_core/pipeline-template/nextflow.config

@@ -186,18 +186,11 @@ profiles {
 
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load {{ name }} custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
-}
+// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
 {% endif -%}
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile

nf_core/pipelines/lint/nextflow_config.py

@@ -346,26 +346,40 @@ 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
-        lines = [
+        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"''',
+        ]
         path = Path(self.wf_path, "nextflow.config")
         i = 0
         with open(path) as f:
             for line in f:
-                if lines[i] in line:
+                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)
+                )
+            )
         else:
             lines[2] = f"\t{lines[2]}"
             lines[4] = f"\t{lines[4]}"

tests/utils.py

@@ -104,7 +104,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]:
     tmp_dir = Path(tempfile.TemporaryDirectory().name)
     root_repo_dir = Path(__file__).resolve().parent.parent
     template_dir = root_repo_dir / "nf_core" / "pipeline-template"
-    pipeline_name = "mypipeline"
+    pipeline_name = "testpipeline"
     pipeline_dir = tmp_dir / pipeline_name
     pipeline_dir.mkdir(parents=True)
 
@@ -114,7 +114,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]:
         org_path="nf-core",
         lint=None,
         template=NFCoreTemplateConfig(
-            name="mypipeline",
+            name="testpipeline",
             author="me",
             description="it is mine",
             org="nf-core",