From 09eaf8f62781c3d54ec02e3db266a16358fa178d Mon Sep 17 00:00:00 2001
From: simonleandergrimm <simonleandergrimm@gmail.com>
Date: Mon, 9 Dec 2024 23:32:14 +0000
Subject: [PATCH] Adding filtlong to the Cleaning step.

---
 subworkflows/local/clean/main.nf | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/clean/main.nf b/subworkflows/local/clean/main.nf
index 9f1e638e..4436b5a7 100644
--- 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
 }
\ No newline at end of file