Reduce output to only the cluster stats file

genepi · Jul 25, 2024 · 8392a21 · 8392a21
1 parent 7135f82
commit 8392a21
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git 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
@@ -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" : ""