Remove all outputs to reduce needed disk storage

genepi · Jul 25, 2024 · a1a7097 · a1a7097
1 parent 105308d
commit a1a7097
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Showing 4 changed files with 0 additions and 5 deletions.
diff --git a/lib/processes/cluster.nf b/lib/processes/cluster.nf
@@ -2,8 +2,6 @@ consensus_fasta="consensus.fasta"
 vsearch_dir="vsearch_clusters"
 
 process CLUSTER {
-    publishDir "${params.output}/${sample}/clustering/${type}", pattern: "${consensus_fasta}", mode: 'copy'
-    publishDir "${params.output}/${sample}/clustering/${type}", pattern: "cluster*", mode: 'copy'
 
     input:
         tuple val( sample ), val( target ), path( detected_umis_fastq )

diff --git a/lib/processes/map_reads.nf b/lib/processes/map_reads.nf
@@ -1,5 +1,4 @@
 process MAP_READS {
-    publishDir "${params.output}/${sample}/align/${type}", mode: 'copy'
 
     input:
         tuple val( sample ), val( target ), path( consensus_fastq )

diff --git a/lib/processes/reformat_filter_cluster.nf b/lib/processes/reformat_filter_cluster.nf
@@ -1,6 +1,5 @@
 process REFORMAT_FILTER_CLUSTER {
     tag "${sample}"
-    publishDir "${params.output}/${sample}/clustering/${type}/smolecule", pattern: "smolecule*", mode: 'copy'
     publishDir "${params.output}/${sample}/stats/${type}", pattern: "*tsv", mode: 'copy'
 
     input:

diff --git a/lib/processes/split_reads.nf b/lib/processes/split_reads.nf
@@ -1,6 +1,5 @@
 process SPLIT_READS {
     publishDir "${params.output}/${sample}/stats/${type}", mode: 'copy', pattern: "*.tsv"
-    publishDir "${params.output}/${sample}/${params.output_format}_filtered/${type}", mode: 'copy', pattern: "*${params.output_format}"
 
     input:
         tuple val( sample ), val( target ), path ( bam ) , path ( bam_bai )