Parse quoted CSV headers

FredHutch · Feb 5, 2024 · d68dcb2 · d68dcb2
1 parent a7ff2a8
commit d68dcb2
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/modules/find_reads.nf b/modules/find_reads.nf
@@ -17,10 +17,10 @@ workflow find_reads {
             )
             .map {
                 it -> [
-                    it['sample'],
+                    it.get('sample', it['"sample"']),
                     [
-                        file(it.get('R1', it['fastq_1']), checkIfExists: true),
-                        file(it.get('R2', it['fastq_2']), checkIfExists: true)
+                        file(it.get('R1', it.get('fastq_1', it['"fastq_1"'])), checkIfExists: true),
+                        file(it.get('R2', it.get('fastq_2', it['"fastq_2"'])), checkIfExists: true)
                     ]
                 ]
             }