Adding filtlong to the Cleaning step.

naobservatory · Dec 9, 2024 · 09eaf8f · 09eaf8f
1 parent 66569ad
commit 09eaf8f
Showing 1 changed file with 12 additions and 4 deletions.
diff --git a/subworkflows/local/clean/main.nf b/subworkflows/local/clean/main.nf
@@ -7,7 +7,11 @@
 ***************************/
 
 include { QC } from "../../../subworkflows/local/qc"
-include { FASTP } from "../../../modules/local/fastp"
+if (params.ont) {
+    include { FILTLONG as FILTER_READS } from "../../../modules/local/filtlong"
+} else {
+    include { FASTP as FILTER_READS } from "../../../modules/local/fastp"
+}
 
 /***********
 | WORKFLOW |
@@ -22,9 +26,13 @@ workflow CLEAN {
         stage_label
         single_end
     main:
-        fastp_ch = FASTP(reads_ch, adapter_path, single_end)
-        qc_ch = QC(fastp_ch.reads, fastqc_cpus, fastqc_mem, stage_label, single_end)
+        if (params.ont) {
+            filter_ch = FILTER_READS(reads_ch)
+        } else {
+            filter_ch = FILTER_READS(reads_ch, adapter_path, single_end)
+        }
+        qc_ch = QC(filter_ch.reads, fastqc_cpus, fastqc_mem, stage_label, single_end)
     emit:
-        reads = fastp_ch.reads
+        reads = filter_ch.reads
         qc = qc_ch.qc
 }