From 8392a211796d7d870c8ec0602fd6e87c57ec5d98 Mon Sep 17 00:00:00 2001
From: AmstlerStephan <stephan.amstler@student.uibk.ac.at>
Date: Thu, 25 Jul 2024 19:03:25 +0200
Subject: [PATCH] Reduce output to only the cluster stats file

---
 lib/processes/cluster.nf                 | 2 --
 lib/processes/reformat_filter_cluster.nf | 6 +++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/lib/processes/cluster.nf b/lib/processes/cluster.nf
index e253d84..22f3249 100644
--- a/lib/processes/cluster.nf
+++ b/lib/processes/cluster.nf
@@ -1,8 +1,6 @@
 consensus_fasta="consensus.fasta"
 detected_umis_file_name="detected_umis.fastq"
 process CLUSTER {
-    publishDir "${params.output}/${sample.baseName}/clustering/${type}", pattern: "cluster*", mode: 'copy'
-        
     input:
         path sample
         val ( type )
diff --git a/lib/processes/reformat_filter_cluster.nf b/lib/processes/reformat_filter_cluster.nf
index 7e5959e..ad5002f 100644
--- a/lib/processes/reformat_filter_cluster.nf
+++ b/lib/processes/reformat_filter_cluster.nf
@@ -8,9 +8,9 @@ process REFORMAT_FILTER_CLUSTER {
         path umi_parse_clusters_python
 
     output:
-        tuple val( "${sample}" ), val( "${target}" ), path( "smolecule*"), optional: true, emit: smolecule_cluster_fastqs
-        tuple val( sample ), val ( target ), path( "*.tsv" ), optional: true
-        tuple val( "${sample}" ), val( "${target}" ), path( "cluster*"), optional: true
+        tuple val( "${sample}" ), path( "smolecule*"), optional: true, emit: smolecule_cluster_fastqs
+        tuple val( "${sample}" ), path( "*.tsv" ), optional: true
+        tuple val( "${sample}" ), path( "cluster*"), optional: true
 
     script:
         def balance_strands = params.balance_strands ? "--balance_strands" : ""