Merge pull request #63 from koenbossers/fix/allow-quoted-fields-in-csv

Allow quoted fields for csv files in .fromSamplesheet()

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Only validate a file with a schema if the file path is provided ([#51](https://github.com/nextflow-io/nf-validation/pull/51))
 - Handle errors when sample sheet not provided or doesn't have a schema ([#56](https://github.com/nextflow-io/nf-validation/pull/56))
 - Silently ignore samplesheet fields that are not defined in samplesheet schema ([#59](https://github.com/nextflow-io/nf-validation/pull/59))
+- Correctly handle double-quoted fields containing commas in csv files by `.fromSamplesheet()` [#63](https://github.com/nextflow-io/nf-validation/pull/63))
 
 ## Version 0.2.1
 

plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy

@@ -72,7 +72,7 @@ class SamplesheetConverter {
         }
         else {
             Path fileSamplesheet = Nextflow.file(samplesheetFile) as Path
-            samplesheetList = fileSamplesheet.splitCsv(header:true, strip:true, sep:delimiter)
+            samplesheetList = fileSamplesheet.splitCsv(header:true, strip:true, sep:delimiter, quote:'"')
         }
 
         // Field checks + returning the channels
@@ -279,4 +279,4 @@ class SamplesheetConverter {
     ) {
         return "Entry ${this.getCount()}: ${message}".toString()
     }
-}
+}