adapt publishing

genepi · Jul 25, 2024 · 877f052 · 877f052
1 parent 79b8c93
commit 877f052
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diff --git 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
@@ -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 //
 ////////////////////