From 877f0521948e89d5a71a69b93f61da868cb37c9e Mon Sep 17 00:00:00 2001
From: AmstlerStephan <stephan.amstler@student.uibk.ac.at>
Date: Thu, 25 Jul 2024 14:16:06 +0200
Subject: [PATCH] adapt publishing

---
 lib/processes/cluster.nf      | 2 +-
 lib/workflows/umi-pipeline.nf | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/processes/cluster.nf b/lib/processes/cluster.nf
index 1142ef5..303081e 100644
--- a/lib/processes/cluster.nf
+++ b/lib/processes/cluster.nf
@@ -2,7 +2,7 @@ consensus_fasta="consensus.fasta"
 vsearch_dir="vsearch_clusters"
 detected_umis_file_name="dected_umis.fastq"
 process CLUSTER {
-    publishDir "${params.output}/${sample}/clustering/${type}", pattern: "cluster*", mode: 'copy'
+    publishDir "${params.output}/${sample.baseName}/clustering/${type}", pattern: "cluster*", mode: 'copy'
         
     input:
         path sample
diff --git a/lib/workflows/umi-pipeline.nf b/lib/workflows/umi-pipeline.nf
index 86d8cdc..07b21c3 100644
--- a/lib/workflows/umi-pipeline.nf
+++ b/lib/workflows/umi-pipeline.nf
@@ -35,6 +35,8 @@ Channel.fromPath("${params.input}/*", type: 'dir')
     .filter( ~/.*barcode(([0-9][0-9]))/ )
     .set { detected_umis_ch }
 
+detected_umis_ch.view()
+
 ////////////////////
 // BEGIN PIPELINE //
 ////////////////////