Merge pull request #10 from TRON-Bioinformatics/dev

Update main.nf

Author: ozlemmuslu

subworkflows/parse_samplesheet/main.nf

@@ -35,8 +35,9 @@ workflow PARSE_SAMPLESHEET {
     validateSamplesheet(ch_samplesheet)
     log.info "[INFO] Samplesheet validated"
 
+    def sep = ch_samplesheet_file.name.endsWith('.tsv') ? '\t' : ','
     ch_samplesheet
-        .splitCsv(header: true)
+        .splitCsv(header: true, sep: sep)
         .map { row ->
 
             def tumorPath = row.tumor_bam.trim()
@@ -49,9 +50,10 @@ workflow PARSE_SAMPLESHEET {
             tuple(row.sample_name, row.pair_identifier, tumorFile, normalFile)
         }
         .set { sample_info_ch }
+
 
     emit:
 
     ch_samples = sample_info_ch
 
-}
+}