Added logic to check if grouping variable matches what is in the inpu…

…t csv file, and added a test samplesheet with grouping

test-data/grouping-samplesheet.csv

@@ -0,0 +1,2 @@
+sample,fastq_1,fastq_2,group
+gold_standard,s3://nao-testing/gold-standard-test/raw/gold_standard_R1.fastq.gz,s3://nao-testing/gold-standard-test/raw/gold_standard_R2.fastq.gz,gold_standard

workflows/run.nf

@@ -30,6 +30,16 @@ workflow RUN {
     kraken_db_path = "${params.ref_dir}/results/kraken_db"
     blast_db_path = "${params.ref_dir}/results/${params.blast_db_prefix}"
 
+    // Check if grouping column exists in samplesheet
+    check_grouping = new File(params.sample_sheet).text.readLines()[0].contains('group') ? true : false
+    if (params.grouping != check_grouping) {
+        if (params.grouping && !check_grouping) {
+            throw new Exception("Grouping column not found in samplesheet")
+        } else if (!params.grouping && check_grouping) {
+            throw new Exception("Grouping column found in samplesheet but not requested")
+        }
+    }
+
     // Prepare samplesheet
     if ( params.grouping ) {
         samplesheet = Channel