Merge branch 'testdata' of https://github.com/drpatelh/nf-core-demult…

…iplex into testdata
nf-core · Jun 5, 2023 · c16411c · c16411c
2 parents 40fdad3 + de32c26
commit c16411c
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#103](https://github.com/nf-core/demultiplex/issues/103) `-profile test` failing due to relative path in `flowcell_input.csv`
+- [#122](https://github.com/nf-core/demultiplex/pull/122) Fails gracefully if an error is encountered
 
 ## 1.3.0 - 2023-05-31
 

diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
@@ -21,7 +21,7 @@ def checkPathParamList = [
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
+if (params.input) { ch_input = file(params.input) } else { Nextflow.error 'Input samplesheet not specified!' }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -192,7 +192,7 @@ workflow DEMULTIPLEX {
             ch_versions = ch_versions.mix(SINGULAR_DEMULTIPLEX.out.versions)
             break
         default:
-            exit 1, "Unknown demultiplexer: ${demultiplexer}"
+            Nextflow.error "Unknown demultiplexer: ${demultiplexer}"
     }
     ch_raw_fastq.dump(tag: "DEMULTIPLEX::Demultiplexed Fastq",{FormattingService.prettyFormat(it)})
 
@@ -321,14 +321,14 @@ def extract_csv(input_csv, input_schema=null) {
                     diff in all_columns ? missing_columns.add(diff) : wrong_columns.add(diff)
                 }
                 if(missing_columns.size() > 0){
-                    exit 1, "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
+                    Nextflow.error "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
                 }
                 else {
-                    exit 1, "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
+                    Nextflow.error "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
                 }
             }
             else {
-                exit 1, "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
+                Nextflow.error "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
             }
 
         }
@@ -345,7 +345,7 @@ def extract_csv(input_csv, input_schema=null) {
             row[column] ?: missing_mandatory_columns.add(column)
         }
         if(missing_mandatory_columns.size > 0){
-            exit 1, "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
+            Nextflow.error "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
         }
 
         def output = []
@@ -355,7 +355,7 @@ def extract_csv(input_csv, input_schema=null) {
             content = row[key]
 
             if(!(content ==~ col.value['pattern']) && col.value['pattern'] != '' && content != '') {
-                exit 1, "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
+                Nextflow.error "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
             }
 
             if(col.value['content'] == 'path'){