From 74a243abf676ac28ba2a85e22183fcd88f09f62f Mon Sep 17 00:00:00 2001
From: Fabian Boehm <Fabian.Boehm@Logartis.de>
Date: Thu, 1 Aug 2024 12:31:27 +0200
Subject: [PATCH] removed debugging statements

---
 conf/modules.config                | 4 ++--
 subworkflows/local/benchmarking.nf | 2 --
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5aead744..fc89e216 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -342,8 +342,8 @@ process {
     }
 
     withName: '.*:FIND_CIRC:UNIFY' {
-        // Keep only rows with UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18
-        ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'"
+        // Keep only rows with CIRCULAR, UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18
+        ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'"
         ext.suffix = "find_circ.bed"
         publishDir = [
             path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" },
diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf
index a1de025a..660ca896 100644
--- a/subworkflows/local/benchmarking.nf
+++ b/subworkflows/local/benchmarking.nf
@@ -34,8 +34,6 @@ workflow BENCHMARKING {
                             benchmarking: meta.benchmarking], bed]}
         .groupTuple()
 
-    ch_all.view {"all: $it"}
-
     SORT(ch_all)
 
     BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed ->