Merge pull request #2211 from awgymer/lint-system-exit

Lint check for `System.exit` calls

docs/api/_src/pipeline_lint_tests/system_exit.md

@@ -0,0 +1,5 @@
+# system_exit
+
+```{eval-rst}
+.. automethod:: nf_core.lint.PipelineLint.system_exit
+```

nf_core/lint/__init__.py

@@ -181,6 +181,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .schema_description import schema_description
     from .schema_lint import schema_lint
     from .schema_params import schema_params
+    from .system_exit import system_exit
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
@@ -223,6 +224,7 @@ def _get_all_lint_tests(release_mode):
             "template_strings",
             "schema_lint",
             "schema_params",
+            "system_exit",
             "schema_description",
             "actions_schema_validation",
             "merge_markers",

nf_core/lint/system_exit.py

@@ -0,0 +1,37 @@
+import logging
+from pathlib import Path
+
+log = logging.getLogger(__name__)
+
+
+def system_exit(self):
+    """Check for System.exit calls in groovy/nextflow code
+
+    Calls to System.exit(1) should be replaced by throwing errors
+
+    This lint test looks for all calls to `System.exit`
+    in any file with the `.nf` or `.groovy` extension
+    """
+    passed = []
+    warned = []
+
+    root_dir = Path(self.wf_path)
+
+    # Get all groovy and nf files
+    groovy_files = [f for f in root_dir.rglob("*.groovy")]
+    nf_files = [f for f in root_dir.rglob("*.nf")]
+    to_check = nf_files + groovy_files
+
+    for file in to_check:
+        try:
+            with file.open() as fh:
+                for i, l in enumerate(fh.readlines(), start=1):
+                    if "System.exit" in l and not "System.exit(0)" in l:
+                        warned.append(f"`System.exit` in {file.name}: _{l.strip()}_  [line {i}]")
+        except FileNotFoundError:
+            log.debug(f"Could not open file {file.name} in system_exit lint test")
+
+    if len(warned) == 0:
+        passed.append("No `System.exit` calls found")
+
+    return {"passed": passed, "warned": warned}

nf_core/pipeline-template/lib/NfcoreSchema.groovy

@@ -2,6 +2,7 @@
 // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
 //
 
+import nextflow.Nextflow
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
 import org.everit.json.schema.ValidationException
@@ -177,7 +178,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            System.exit(1)
+            Nextflow.error('Exiting!')
         }
     }
 

nf_core/pipeline-template/lib/WorkflowMain.groovy

@@ -2,6 +2,8 @@
 // This file holds several functions specific to the main.nf workflow in the {{ name }} pipeline
 //
 
+import nextflow.Nextflow
+
 class WorkflowMain {
 
     //
@@ -85,8 +87,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
-            System.exit(1)
+            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
         }
     }
     {% if igenomes -%}

nf_core/pipeline-template/lib/WorkflowPipeline.groovy

@@ -2,6 +2,7 @@
 // This file holds several functions specific to the workflow/{{ short_name }}.nf in the {{ name }} pipeline
 //
 
+import nextflow.Nextflow
 import groovy.text.SimpleTemplateEngine
 
 class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
@@ -15,8 +16,7 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
 {% endif %}
 
         if (!params.fasta) {
-            log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-            System.exit(1)
+            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
         }
     }
 
@@ -70,12 +70,12 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} {
     //
     private static void genomeExistsError(params, log) {
         if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
                 "  Currently, the available genome keys are:\n" +
                 "  ${params.genomes.keySet().join(", ")}\n" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            System.exit(1)
+            Nextflow.error(error_string)
         }
     }
 {% endif -%}}