From 5c4d02263be3cfd927d594d365702d5c162808ab Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:32:29 -0500
Subject: [PATCH] refactor: Replace custom publish dirs with reference to
 task.process

---
 modules/haplink/variants/main.nf | 2 +-
 modules/shorah/amplicon/main.nf  | 2 +-
 modules/shorah/shotgun/main.nf   | 2 +-
 modules/viquas/main.nf           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index 9f036de..b4f7149 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -11,7 +11,7 @@ process HAPLINK_VARIANTS {
     output:
     tuple val(prefix), path("*.vcf")
 
-    publishDir "results", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
index 5c68ca1..d35961a 100644
--- a/modules/shorah/amplicon/main.nf
+++ b/modules/shorah/amplicon/main.nf
@@ -12,7 +12,7 @@ process SHORAH_AMPLICON {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/shorah-amplicon", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/shorah/shotgun/main.nf b/modules/shorah/shotgun/main.nf
index 89b8ef7..224dca9 100644
--- a/modules/shorah/shotgun/main.nf
+++ b/modules/shorah/shotgun/main.nf
@@ -12,7 +12,7 @@ process SHORAH_SHOTGUN {
     tuple val(prefix), path("*.vcf")
     tuple val(prefix), path("*support.fas")
 
-    publishDir "results/shorah-shotgun", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """
diff --git a/modules/viquas/main.nf b/modules/viquas/main.nf
index 16bb7b5..ab467a3 100644
--- a/modules/viquas/main.nf
+++ b/modules/viquas/main.nf
@@ -11,7 +11,7 @@ process VIQUAS {
     output:
     tuple val(prefix), path("*.fa")
 
-    publishDir "results/viquas", mode: 'copy'
+    publishDir "results/${task.process}", mode: 'copy'
 
     script:
     """