Stop optional columns with commas causing incorrect CSV parsing

resolves nf-core#30
grunwaldlab · Oct 13, 2023 · 05a2895 · 05a2895
1 parent 780d52a
commit 05a2895
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -16,7 +16,7 @@
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.[ct]sv$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/plantpathsurveil/usage#samplesheet-input).",

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -12,7 +12,7 @@ workflow INPUT_CHECK {
     SAMPLESHEET_CHECK ( samplesheet )
     SAMPLESHEET_CHECK.out
         .csv
-        .splitCsv ( header:true, sep:',' )
+        .splitCsv ( header:true, sep:',', quote:'"')
         .map { create_reads_ref_channel(it) }
         .transpose ( by: 4 ) // Duplicate rows for each group when there are multiple groups per sample
         .map { it[0..3] + [[id: it[4]]] }