Merge pull request #107 from sanger-tol/fix_splitCsv_in_fetch_input.nf

Fix split csv in fetch input.nf
sanger-tol · Jul 31, 2024 · 50e5431 · 50e5431
2 parents 5420de2 + a8e2bba
commit 50e5431
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diff --git 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
@@ -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]]