chore: Remove all publishDir and cache stuff

modules/primer3_calc/main.nf

@@ -1,7 +1,5 @@
 process primer3_calc {
     conda "primer3"
-    publishDir "results/${task.process}", overwrite:'true'
-    cache 'deep'
     tag "${conf.baseName.replaceFirst(/\.primer3\$/, '')}"
 
     input:

modules/primer3_conf/main.nf

@@ -1,6 +1,4 @@
 process primer3_conf {
-    publishDir "results/${task.process}", overwrite:'true'
-    cache 'deep'
     conda "seqkit"
     tag "${target.baseName.replaceFirst(/\.primer3/, '')}"
 

modules/primer3_index/main.nf

@@ -1,7 +1,5 @@
 process primer3_index {
     conda "genometester4"
-    publishDir "results/${task.process}",overwrite:'true'
-    cache 'deep'
     tag "$fasta.baseName"
 
     input:

modules/primer3_results2fasta/main.nf

@@ -1,6 +1,4 @@
 process primer3_results2fasta {
-    publishDir "results/${task.process}", overwrite:'true'
-    cache 'deep'
     tag "$results.baseName"
 
     input:

nextflow.config

@@ -2,6 +2,7 @@ params {
     input = null
     fasta = null
     targetseq = null
+    outdir = "results"
 }
 
 docker.enabled = true
@@ -37,3 +38,13 @@ profiles {
 plugins {
     id '[email protected]'
 }
+
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+}