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nf-core · Jul 22, 2020 · 47c7bfc · 47c7bfc
1 parent f4e8a78
commit 47c7bfc
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -1333,7 +1333,8 @@ if (params.umi){
   else input_pair_reads_sentieon.close()
 }
 else {
-  inputPairReads = outputPairReadsTrimGalore.mix(inputBam)
+  if (params.trim_fastq) inputPairReads = outputPairReadsTrimGalore
+  else inputPairReads = inputPairReads.mix(inputBam)
   inputPairReads = inputPairReads.dump(tag:'INPUT')
 
   (inputPairReads, input_pair_reads_sentieon) = inputPairReads.into(2)