Remove exit statements

.nf-core.yml

@@ -10,4 +10,5 @@ lint:
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png
     - lib/NfcoreTemplate.groovy
+    - lib/NfcoreSchema.groovy
   template_strings: False

CHANGELOG.md

@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#941](https://github.com/nf-core/sarek/pull/941) - Fix json validation for `tools`, `skip_tools` and `use_gatk_spark` [#892](https://github.com/nf-core/sarek/issues/892)
 - [#954](https://github.com/nf-core/sarek/pull/954) - Fix missing annotation keys with snpeff and ensemblvep for `hg19`
 - [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible
+- [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead
 
 ### Deprecated
 

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!')
         }
     }
 

lib/WorkflowSarek.groovy

@@ -2,6 +2,7 @@
 // This file holds several functions specific to the workflow/sarek.nf in the nf-core/sarek pipeline
 //
 
+import nextflow.Nextflow
 import groovy.text.SimpleTemplateEngine
 
 class WorkflowSarek {
@@ -14,8 +15,7 @@ class WorkflowSarek {
 
 
         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.")
         }
     }
 
@@ -66,39 +66,38 @@ class WorkflowSarek {
     //
     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)
         }
     }
 
     public static String retrieveInput(params, log){
         if (!params.build_only_index) {
             switch (params.step) {
-                case 'mapping':                 log.warn "Can't start with step $params.step without samplesheet"
-                                                System.exit(1);
+                case 'mapping':                 Nextflow.error("Can't start with step $params.step without samplesheet")
                                                 break
-                case 'markduplicates':          log.warn "Using file ${params.outdir}/csv/mapped.csv"
+                case 'markduplicates':          log.warn("Using file ${params.outdir}/csv/mapped.csv")
                                                 params.putIfAbsent("input","${params.outdir}/csv/mapped.csv");
                                                 break
-                case 'prepare_recalibration':   log.warn "Using file ${params.outdir}/csv/markduplicates_no_table.csv"
+                case 'prepare_recalibration':   log.warn("Using file ${params.outdir}/csv/markduplicates_no_table.csv")
                                                 params.putIfAbsent("input", "${params.outdir}/csv/markduplicates_no_table.csv");
                                                 break
-                case 'recalibrate':             log.warn "Using file ${params.outdir}/csv/markduplicates.csv"
+                case 'recalibrate':             log.warn("Using file ${params.outdir}/csv/markduplicates.csv")
                                                 params.putIfAbsent("input", "${params.outdir}/csv/markduplicates.csv");
                                                 break
-                case 'variant_calling':         log.warn "Using file ${params.outdir}/csv/recalibrated.csv"
+                case 'variant_calling':         log.warn("Using file ${params.outdir}/csv/recalibrated.csv")
                                                 params.putIfAbsent("input", "${params.outdir}/csv/recalibrated.csv");
                                                 break
                 // case 'controlfreec':         csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
-                case 'annotate':                log.warn "Using file ${params.outdir}/csv/variantcalled.csv"
+                case 'annotate':                log.warn("Using file ${params.outdir}/csv/variantcalled.csv")
                                                 params.putIfAbsent("input","${params.outdir}/csv/variantcalled.csv");
                                                 break
-                default:                        log.warn "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
-                                                exit 1, "Unknown step $params.step"
+                default:                        log.warn("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
+                                                Nextflow.error("Unknown step $params.step")
             }
         }
     }