Parse quoted filepaths

FredHutch · Feb 5, 2024 · c5abae8 · c5abae8
1 parent c18d491
commit c5abae8
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/modules/find_reads.nf b/modules/find_reads.nf
@@ -19,8 +19,8 @@ workflow find_reads {
                 it -> [
                     it.get('sample', it['"sample"']),
                     [
-                        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)
+                        file(it.get('R1', it.get('fastq_1', it['"fastq_1"']).replaceAll(/^\"|\"$/, "")), checkIfExists: true),
+                        file(it.get('R2', it.get('fastq_2', it['"fastq_2"']).replaceAll(/^\"|\"$/, "")), checkIfExists: true)
                     ]
                 ]
             }