From 93bd5cedec451ec13286a226141bf207eb7de57f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 18 Oct 2023 21:40:08 -0500
Subject: [PATCH] chore: Replace results dir with parameterized outdir

---
 modules/cliquesnv/main.nf          | 2 +-
 modules/efetch/main.nf             | 2 +-
 modules/haplink/haplotypes/main.nf | 2 +-
 modules/haplink/sequences/main.nf  | 2 +-
 modules/haplink/variants/main.nf   | 2 +-
 modules/minimap2/main.nf           | 2 +-
 modules/quasirecomb/main.nf        | 2 +-
 modules/shorah/amplicon/main.nf    | 2 +-
 modules/shorah/shotgun/main.nf     | 2 +-
 modules/viquas/main.nf             | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
index da197e7..bcccabf 100644
--- a/modules/cliquesnv/main.nf
+++ b/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
diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index f3ce0b3..3fb7e9a 100644
--- a/modules/efetch/main.nf
+++ b/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'
diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
index dc84ef8..dedc30b 100644
--- a/modules/haplink/haplotypes/main.nf
+++ b/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
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index ed6f6a6..77801cd 100644
--- a/modules/haplink/sequences/main.nf
+++ b/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
diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index f467f77..995edfa 100644
--- a/modules/haplink/variants/main.nf
+++ b/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
diff --git a/modules/minimap2/main.nf b/modules/minimap2/main.nf
index 7d3c2aa..4b39349 100644
--- a/modules/minimap2/main.nf
+++ b/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")
diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
index 8e054cf..824a47a 100644
--- a/modules/quasirecomb/main.nf
+++ b/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
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index f37d70c..3c8e373 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/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
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 2b7aa86..0fb73cb 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/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
diff --git a/modules/viquas/main.nf b/modules/viquas/main.nf
index ad19953..440161b 100644
--- a/modules/viquas/main.nf
+++ b/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