chore: Replace results dir with parameterized outdir

modules/cliquesnv/main.nf

@@ -13,7 +13,7 @@ process CLIQUESNV {
     tuple val(prefix), path("*.json")
     tuple val(prefix), path("*.fasta")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/efetch/main.nf

@@ -7,7 +7,7 @@ process EFETCH {
     input:
     val(genome)
 
-    publishDir "results", mode: 'copy'
+    publishDir "${params.outdir}", mode: 'copy'
 
     output:
     path 'reference.fasta'

modules/haplink/haplotypes/main.nf

@@ -12,7 +12,7 @@ process HAPLINK_HAPLOTYPES {
     output:
     tuple val(prefix), path("*.yaml")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/haplink/sequences/main.nf

@@ -12,7 +12,7 @@ process HAPLINK_SEQUENCES {
     output:
     tuple val(prefix), val(method), path("*.fasta")
 
-    publishDir "results/${method}", mode: 'copy'
+    publishDir "${params.outdir}/${method}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/haplink/variants/main.nf

@@ -12,7 +12,7 @@ process HAPLINK_VARIANTS {
     output:
     tuple val(prefix), path("*.vcf")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/minimap2/main.nf

@@ -8,7 +8,7 @@ process MINIMAP2 {
     tuple val(prefix), path(reads)
     path reference
 
-    publishDir "results", mode: 'copy'
+    publishDir "${params.outdir}", mode: 'copy'
 
     output:
     tuple val(prefix), path("*.bam"), path("*.bam.bai")

modules/quasirecomb/main.nf

@@ -11,7 +11,7 @@ process QUASIRECOMB {
     output:
     tuple val(prefix), path("*.fasta")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/shorah/amplicon/main.nf

@@ -13,7 +13,7 @@ process SHORAH_AMPLICON {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/shorah/shotgun/main.nf

@@ -13,7 +13,7 @@ process SHORAH_SHOTGUN {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when

modules/viquas/main.nf

@@ -12,7 +12,7 @@ process VIQUAS {
     output:
     tuple val(prefix), path("*.fa")
 
-    publishDir "results/${task.process}", mode: 'copy'
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
 
     when:
     task.ext.when == null || task.ext.when