Preserve compatibility with R1/R2

FredHutch · Mar 13, 2024 · b96d37b · b96d37b
1 parent 2d86d42
commit b96d37b
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"']).replaceAll(/^\"|\"$/, ""),
                     [
-                        file(it.get('R1', it.get('fastq_1', it['"fastq_1"']).replaceAll(/^\"|\"$/, "")), checkIfExists: true),
-                        file(it.get('R2', it.get('fastq_2', it['"fastq_2"']).replaceAll(/^\"|\"$/, "")), checkIfExists: true)
+                        file(it.get('R1', it.get('fastq_1', it.get('"fastq_1"', 'none')).replaceAll(/^\"|\"$/, "")), checkIfExists: true),
+                        file(it.get('R2', it.get('fastq_2', it.get('"fastq_2"', 'none')).replaceAll(/^\"|\"$/, "")), checkIfExists: true)
                     ]
                 ]
             }