Fix: Remove all system.exit(1) from code and replace with correct error

nf-core · Aug 1, 2023 · 3d99354 · 3d99354
1 parent 750dfe6
commit 3d99354
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Showing 7 changed files with 43 additions and 67 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### 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/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
@@ -177,7 +177,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            System.exit(1)
+            Nextflow.error("")
         }
     }
 

diff --git a/lib/WorkflowCommons.groovy b/lib/WorkflowCommons.groovy
@@ -9,12 +9,11 @@ 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 +120,13 @@ 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
@@ -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
@@ -84,18 +84,15 @@ 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 +117,30 @@ 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
@@ -12,50 +12,41 @@ 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")
             }
         }
     }

diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
@@ -180,8 +180,8 @@ workflow NANOPORE {
                 .filter { it[1] == null }
                 .filter { it[-1] >= params.min_barcode_reads }
                 .map { it -> [ "${it[0]}\t${it[-1]}" ] }
-                .collect()                
-                .map { 
+                .collect()
+                .map {
                     tsv_data ->
                         def header = ['Barcode', 'Read count']
                         WorkflowCommons.multiqcTsvFromList(tsv_data, header)
@@ -194,8 +194,8 @@ workflow NANOPORE {
             ch_fastq_dirs
                 .filter { it[-1] == null }
                 .map { it -> [ "${it[1]}\t${it[0]}" ] }
-                .collect()                
-                .map { 
+                .collect()
+                .map {
                     tsv_data ->
                         def header = ['Sample', 'Missing barcode']
                         WorkflowCommons.multiqcTsvFromList(tsv_data, header)
@@ -218,8 +218,7 @@ workflow NANOPORE {
             .map { it -> [ 'SAMPLE_1', 'single_barcode', it, 10000000 ] }
             .set{ ch_fastq_dirs }
     } else {
-        log.error "Please specify a valid folder containing ONT basecalled, barcoded 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)
+        error "Please specify a valid folder containing ONT basecalled, barcoded fastq files generated by guppy_barcoder or guppy_basecaller e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/"
     }
 
     //
@@ -239,7 +238,7 @@ workflow NANOPORE {
     ch_pass_fail_barcode_count
         .fail
         .collect()
-        .map { 
+        .map {
             tsv_data ->
                 def header = ['Sample', 'Barcode count']
                 WorkflowCommons.multiqcTsvFromList(tsv_data, header)
@@ -278,7 +277,7 @@ workflow NANOPORE {
     ch_pass_fail_guppyplex_count
         .fail
         .collect()
-        .map { 
+        .map {
             tsv_data ->
                 def header = ['Sample', 'Read count']
                 WorkflowCommons.multiqcTsvFromList(tsv_data, header)
@@ -410,13 +409,13 @@ workflow NANOPORE {
         NEXTCLADE_RUN
             .out
             .csv
-            .map { 
+            .map {
                 meta, csv ->
                     def clade = WorkflowCommons.getNextcladeFieldMapFromCsv(csv)['clade']
                     return [ "$meta.id\t$clade" ]
             }
-            .collect()                
-            .map { 
+            .collect()
+            .map {
                 tsv_data ->
                     def header = ['Sample', 'clade']
                     WorkflowCommons.multiqcTsvFromList(tsv_data, header)