reorder trimmomatic base crop stuff

theiagen · Nov 18, 2024 · b8d7d96 · b8d7d96
1 parent 563f6d2
commit b8d7d96
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tasks/quality_control/read_filtering/task_trimmomatic.wdl b/tasks/quality_control/read_filtering/task_trimmomatic.wdl
@@ -40,9 +40,9 @@ task trimmomatic_pe {
     -threads ~{cpu} \
     ~{read1} ~{read2} \
     -baseout ~{samplename}.fastq.gz \
+    "${CROPPING_VAR}" \
     SLIDINGWINDOW:~{trimmomatic_window_size}:~{trimmomatic_quality_trim_score} \
-    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt \
-    "${CROPPING_VAR}"
+    MINLEN:~{trimmomatic_min_length} &> ~{samplename}.trim.stats.txt
 
   >>>
   output {