From e83114729fcb28abc5fe4fc38dc78b202c63d192 Mon Sep 17 00:00:00 2001
From: Ge94 <germana.baldi@gmail.com>
Date: Fri, 6 Dec 2024 16:45:12 +0000
Subject: [PATCH] replaced published_contigs variable

---
 subworkflows/local/assembly_qc.nf | 2 +-
 workflows/miassembler.nf          | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/assembly_qc.nf b/subworkflows/local/assembly_qc.nf
index bbb48ad..f743182 100644
--- a/subworkflows/local/assembly_qc.nf
+++ b/subworkflows/local/assembly_qc.nf
@@ -88,6 +88,6 @@ workflow ASSEMBLY_QC {
     )
 
     emit:
-    filtered_contigs = cleaned_contigs
+    cleaned_contigs = cleaned_contigs
     versions         = ch_versions
 }
diff --git a/workflows/miassembler.nf b/workflows/miassembler.nf
index f3104a6..87479e0 100644
--- a/workflows/miassembler.nf
+++ b/workflows/miassembler.nf
@@ -246,7 +246,7 @@ workflow MIASSEMBLER {
 
     // Coverage //
     ASSEMBLY_COVERAGE(
-        ASSEMBLY_QC.out.filtered_contigs.join( READS_QC.out.qc_reads, remainder: false ),
+        ASSEMBLY_QC.out.cleaned_contigs.join( READS_QC.out.qc_reads, remainder: false ),
         READS_QC.out.fastp_json
     )
 
@@ -255,7 +255,7 @@ workflow MIASSEMBLER {
     // Stats //
     /* The QUAST module was modified to run metaQUAST instead */
     QUAST(
-        ASSEMBLY_QC.out.filtered_contigs,
+        ASSEMBLY_QC.out.cleaned_contigs,
         [ [], [] ], // reference
         [ [], [] ]  // gff
     )