Remove publish dirs for intermediate processes

workflow/main.nf

@@ -36,7 +36,6 @@ references = params.references
 process checkDesignFile {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda'
 
   input:
@@ -63,7 +62,6 @@ process checkDesignFile {
 process untarBCL {
 
   tag "${tar}"
-  publishDir "${outDir}/${task.process}", mode: 'copy'
   module 'pigz/2.4'
 
   input:
@@ -114,7 +112,7 @@ if (bclCount.value == 1) {
   process countDesign {
 
     tag "${name}"
-    publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
+    publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
 
     input:
       file fastqs from cellrangerCount.collect()
@@ -137,7 +135,6 @@ process fastqc {
 
   tag "${bclName}"
   queue 'super'
-  publishDir "${outDir}/misc/${task.process}/${name}/${bclName}", mode: 'copy', pattern: "{*fastqc.zip}"
   module 'fastqc/0.11.5:parallel'
 
   input:
@@ -161,7 +158,6 @@ process fastqc {
 process versions {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
 
   input: