Merge pull request nf-core#387 from adamrtalbot/remove_system_exit_1

Remove system exit 1
BU-ISCIII · Aug 16, 2023 · 75d3a6c · 75d3a6c
2 parents 750dfe6 + 94b7f23
commit 75d3a6c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,12 +5,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+### Credits
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+
+### Software dependencies
+
 ### Enhancements & fixes
 
+- [[#387](https://github.com/nf-core/viralrecon/pull/387/files)] - Software closes gracefully when encountering an error
+
 ## [[2.6.0](https://github.com/nf-core/viralrecon/releases/tag/2.6.0)] - 2023-03-23
 
 ### Credits
 
+### Software dependencies
+
 Special thanks to the following for their code contributions to the release:
 
 - [Friederike Hanssen](https://github.com/FriederikeHanssen)

diff --git a/lib/WorkflowCommons.groovy b/lib/WorkflowCommons.groovy
@@ -1,6 +1,7 @@
 //
 // This file holds several functions common to the multiple workflows in the nf-core/viralrecon pipeline
 //
+import nextflow.Nextflow
 
 class WorkflowCommons {
 
@@ -9,12 +10,11 @@ class WorkflowCommons {
     //
     private static void genomeExistsError(params, log) {
         if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            Nextflow.error("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\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)
+                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
         }
     }
 
@@ -121,14 +121,13 @@ class WorkflowCommons {
         def intersect = bed_contigs.intersect(fai_contigs)
         if (intersect.size() != bed_contigs.size()) {
             def diff = bed_contigs.minus(intersect).sort()
-            log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            Nextflow.error("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  Contigs in primer BED file do not match those in the reference genome:\n\n" +
                 "  ${diff.join('\n  ')}\n\n" +
                 "  Please check:\n" +
                 "    - Primer BED file supplied with --primer_bed\n" +
                 "    - Genome FASTA file supplied with --fasta\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            System.exit(1)
+                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
         }
     }
 

diff --git a/lib/WorkflowIllumina.groovy b/lib/WorkflowIllumina.groovy
@@ -1,7 +1,7 @@
 //
 // This file holds several functions specific to the workflow/illumina.nf in the nf-core/viralrecon pipeline
 //
-
+import nextflow.Nextflow
 import groovy.json.JsonSlurper
 
 class WorkflowIllumina {
@@ -14,53 +14,45 @@ class WorkflowIllumina {
 
         // Generic parameter validation
         if (!valid_params['protocols'].contains(params.protocol)) {
-            log.error "Invalid option: '${params.protocol}'. Valid options for '--protocol': ${valid_params['protocols'].join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid option: '${params.protocol}'. Valid options for '--protocol': ${valid_params['protocols'].join(', ')}.")
         }
 
         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.")
         }
 
         if (!params.skip_kraken2 && !params.kraken2_db) {
             if (!params.kraken2_db_name) {
-                log.error "Please specify a valid name to build Kraken2 database for host e.g. '--kraken2_db_name human'."
-                System.exit(1)
+                Nextflow.error("Please specify a valid name to build Kraken2 database for host e.g. '--kraken2_db_name human'.")
             }
         }
 
         // Variant calling parameter validation
         if (params.variant_caller) {
             if (!valid_params['variant_callers'].contains(params.variant_caller)) {
-                log.error "Invalid option: ${params.variant_caller}. Valid options for '--variant_caller': ${valid_params['variant_callers'].join(', ')}."
-                System.exit(1)
+                Nextflow.error("Invalid option: ${params.variant_caller}. Valid options for '--variant_caller': ${valid_params['variant_callers'].join(', ')}.")
             }
         }
 
         // Consensus calling parameter validation
         if (params.consensus_caller) {
             if (!valid_params['consensus_callers'].contains(params.consensus_caller)) {
-                log.error "Invalid option: ${params.consensus_caller}. Valid options for '--consensus_caller': ${valid_params['consensus_callers'].join(', ')}."
-                System.exit(1)
+                Nextflow.error("Invalid option: ${params.consensus_caller}. Valid options for '--consensus_caller': ${valid_params['consensus_callers'].join(', ')}.")
             }
         }
 
         if (params.protocol == 'amplicon' && !params.skip_variants && !params.primer_bed) {
-            log.error "To perform variant calling in amplicon mode please provide a valid primer BED file e.g. '--primer_bed primers.bed'."
-            System.exit(1)
+            Nextflow.error("To perform variant calling in amplicon mode please provide a valid primer BED file e.g. '--primer_bed primers.bed'.")
         }
 
         // Assembly parameter validation
         def assemblers = params.assemblers ? params.assemblers.split(',').collect{ it.trim().toLowerCase() } : []
         if ((valid_params['assemblers'] + assemblers).unique().size() != valid_params['assemblers'].size()) {
-            log.error "Invalid option: ${params.assemblers}. Valid options for '--assemblers': ${valid_params['assemblers'].join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid option: ${params.assemblers}. Valid options for '--assemblers': ${valid_params['assemblers'].join(', ')}.")
         }
 
         if (!valid_params['spades_modes'].contains(params.spades_mode)) {
-            log.error "Invalid option: ${params.spades_mode}. Valid options for '--spades_modes': ${valid_params['spades_modes'].join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid option: ${params.spades_mode}. Valid options for '--spades_modes': ${valid_params['spades_modes'].join(', ')}.")
         }
     }
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -1,6 +1,7 @@
 //
 // This file holds several functions specific to the main.nf workflow in the nf-core/viralrecon pipeline
 //
+import nextflow.Nextflow
 
 class WorkflowMain {
 
@@ -84,18 +85,15 @@ class WorkflowMain {
         // Check sequencing platform
         def platformList = ['illumina', 'nanopore']
         if (!params.platform) {
-            log.error "Platform not specified with e.g. '--platform illumina'. Valid options: ${platformList.join(', ')}."
-            System.exit(1)
+            Nextflow.error("Platform not specified with e.g. '--platform illumina'. Valid options: ${platformList.join(', ')}.")
         } else if (!platformList.contains(params.platform)) {
-            log.error "Invalid platform option: '${params.platform}'. Valid options: ${platformList.join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid platform option: '${params.platform}'. Valid options: ${platformList.join(', ')}.")
         }
 
         // Check Nextclade dataset parameters
         if (!params.skip_consensus && !params.skip_nextclade) {
             if (!params.nextclade_dataset && !params.nextclade_dataset_name) {
-                log.error "Nextclade dataset not specified with '--nextclade_dataset' or '--nextclade_dataset_name'. A list of available datasets can be obtained using the Nextclade 'nextclade dataset list' command."
-                System.exit(1)
+                Nextflow.error("Nextclade dataset not specified with '--nextclade_dataset' or '--nextclade_dataset_name'. A list of available datasets can be obtained using the Nextclade 'nextclade dataset list' command.")
             }
         }
     }
@@ -120,33 +118,30 @@ class WorkflowMain {
                         if (genome_map.containsKey(primer_set_version)) {
                             genome_map = genome_map[ primer_set_version ]
                         } else {
-                            log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                            Nextflow.error("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                                 " --primer_set_version '${primer_set_version}' not found!\n\n" +
                                 " Currently, the available primer set version keys are: ${genome_map.keySet().join(", ")}\n\n" +
                                 " Please check:\n" +
                                 "   - The value provided to --primer_set_version (currently '${primer_set_version}')\n" +
                                 "   - The value provided to --primer_set (currently '${primer_set}')\n" +
                                 "   - The value provided to --genome (currently '${params.genome}')\n" +
-                                "   - Any custom config files provided to the pipeline.\n\n" + support_link
-                            System.exit(1)
+                                "   - Any custom config files provided to the pipeline.\n\n" + support_link)
                         }
                     } else {
-                        log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                        Nextflow.error("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                             " --primer_set '${primer_set}' not found!\n\n" +
                             " Currently, the available primer set keys are: ${genome_map.keySet().join(", ")}\n\n" +
                             " Please check:\n" +
                             "   - The value provided to --primer_set (currently '${primer_set}')\n" +
                             "   - The value provided to --genome (currently '${params.genome}')\n" +
-                            "   - Any custom config files provided to the pipeline.\n\n" + support_link
-                        System.exit(1)
+                            "   - Any custom config files provided to the pipeline.\n\n" + support_link)
                     }
                 } else {
-                    log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                    Nextflow.error("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                         " Genome '${params.genome}' does not contain any primer sets!\n\n" +
                         " Please check:\n" +
                         "   - The value provided to --genome (currently '${params.genome}')\n" +
-                        "   - Any custom config files provided to the pipeline.\n\n" + support_link
-                    System.exit(1)
+                        "   - Any custom config files provided to the pipeline.\n\n" + support_link)
                 }
             }
             if (genome_map.containsKey(attribute)) {

diff --git a/lib/WorkflowNanopore.groovy b/lib/WorkflowNanopore.groovy
@@ -1,6 +1,7 @@
 //
 // This file holds several functions specific to the workflow/nanopore.nf in the nf-core/viralrecon pipeline
 //
+import nextflow.Nextflow
 
 class WorkflowNanopore {
 
@@ -12,50 +13,41 @@ class WorkflowNanopore {
 
         // Generic parameter validation
         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.")
         }
 
         if (!params.primer_bed) {
-            log.error "Primer BED file not specified with e.g. '--primer_bed primers.bed' or via a detectable config file."
-            System.exit(1)
+            Nextflow.error("Primer BED file not specified with e.g. '--primer_bed primers.bed' or via a detectable config file.")
         }
 
         if (!params.artic_scheme) {
-            log.error "ARTIC scheme not specified with e.g. --artic_scheme 'nCoV-2019' or via a detectable config file."
-            System.exit(1)
+            Nextflow.error("ARTIC scheme not specified with e.g. --artic_scheme 'nCoV-2019' or via a detectable config file.")
         }
 
         if (!valid_params['artic_minion_caller'].contains(params.artic_minion_caller)) {
-            log.error "Invalid option: ${params.artic_minion_caller}. Valid options for '--artic_minion_caller': ${valid_params['artic_minion_caller'].join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid option: ${params.artic_minion_caller}. Valid options for '--artic_minion_caller': ${valid_params['artic_minion_caller'].join(', ')}.")
         }
 
         if (!valid_params['artic_minion_aligner'].contains(params.artic_minion_aligner)) {
-            log.error "Invalid option: ${params.artic_minion_aligner}. Valid options for '--artic_minion_aligner': ${valid_params['artic_minion_aligner'].join(', ')}."
-            System.exit(1)
+            Nextflow.error("Invalid option: ${params.artic_minion_aligner}. Valid options for '--artic_minion_aligner': ${valid_params['artic_minion_aligner'].join(', ')}.")
         }
 
         if (!params.fastq_dir) {
-            log.error "Please specify a valid folder containing ONT basecalled fastq files generated by guppy_barcoder or guppy_basecaller e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/"
-            System.exit(1)
+            Nextflow.error("Please specify a valid folder containing ONT basecalled fastq files generated by guppy_barcoder or guppy_basecaller e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/")
         }
 
         if (params.artic_minion_caller == 'nanopolish') {
             if (!params.fast5_dir) {
-                log.error "Please specify a valid folder containing ONT fast5 files e.g. '--fast5_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fast5_pass/"
-                System.exit(1)
+                Nextflow.error("Please specify a valid folder containing ONT fast5 files e.g. '--fast5_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fast5_pass/")
             }
             if (!params.sequencing_summary) {
-                log.error "Please specify a valid ONT sequencing summary file e.g. '--sequencing_summary ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/sequencing_summary.txt"
-                System.exit(1)
+                Nextflow.error("Please specify a valid ONT sequencing summary file e.g. '--sequencing_summary ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/sequencing_summary.txt")
             }
         }
 
         if (params.artic_minion_caller == 'medaka') {
             if (!params.artic_minion_medaka_model) {
-                log.error "Please specify the '--artic_minion_medaka_model' parameter too if using the '--artic_minion_caller medaka' workflow.\nSee https://github.com/nanoporetech/medaka"
-                System.exit(1)
+                Nextflow.error("Please specify the '--artic_minion_medaka_model' parameter too if using the '--artic_minion_caller medaka' workflow.\nSee https://github.com/nanoporetech/medaka")
             }
         }
     }