fixed assembly output dir structure

jimmyliu1326 · Aug 21, 2023 · b0d0f64 · b0d0f64
1 parent 0942537
commit b0d0f64
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/modules/local/nanopore-assembly.nf b/modules/local/nanopore-assembly.nf
@@ -2,7 +2,7 @@
 process metaflye {
     tag "MetaFlye assembly on ${sample_id}"
     label "process_medium"
-    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy"
+    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy", pattern: "*.{log,txt,gfa}"
     errorStrategy 'ignore'
 
     input:
@@ -24,7 +24,7 @@ process metaflye {
 process dragonflye {
     tag "DragonFlye assembly on ${sample_id}"
     label "process_medium"
-    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy"
+    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy", pattern: "*.{log,txt,gfa}"
     errorStrategy 'ignore'
 
     input:

diff --git a/modules/local/nanopore-polish.nf b/modules/local/nanopore-polish.nf
@@ -2,7 +2,7 @@
 process medaka {
     tag "Assembly polishing for ${sample_id}"
     label "process_medium"
-    publishDir "$params.outdir"+"/assembly", mode: "copy"
+    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy"
 
     input:
         tuple val(sample_id), path(assembly), path(reads)
@@ -19,7 +19,7 @@ process medaka_gpu {
     tag "Assembly polishing for ${sample_id}"
     label "process_medium"
     maxForks 1
-    publishDir "$params.outdir"+"/assembly", mode: "copy"
+    publishDir "$params.outdir"+"/assembly/${sample_id}", mode: "copy"
 
     input:
         tuple val(sample_id), path(assembly), path(reads)