diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d2a81c5..7792d887 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ General tidy up of the configuration and the pipeline
 - Removed some options that were not used or not needed
 - All relevant outputs are now copied to the output directory
 - Fixed some blast parameters to match the behaviour of the Snakemake pipeline
+- Fixed parsing of samplesheets from fetchngs to capture correct data type
 
 ### Parameters
 
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index da522ca8..d498269f 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -20,7 +20,7 @@ workflow INPUT_CHECK {
     if ( params.fetchngs_samplesheet ) {
         FETCHNGSSAMPLESHEET_CHECK ( samplesheet )
             .csv
-            .splitCsv ( header:true, sep:',' )
+            .splitCsv ( header:true, sep:',', quote:'"' )
             .branch { row ->
                 paired: row.fastq_2
                     [[id: row.run_accession, row:row], [row.fastq_1, row.fastq_2]]