From 002bd44975c21d508ef6124b69e85164c3826a2a Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:30:24 -0500
Subject: [PATCH] refactor: Change output directory to match haplotypes

---
 main.nf                           | 4 ++--
 modules/haplink/sequences/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 8bc7a7f..e623fa6 100755
--- a/main.nf
+++ b/main.nf
@@ -49,7 +49,7 @@ workflow {
     )
     HAPLINK_RAW_HAPLOTYPES
         .out
-    .map{ [ it[0], 'raw', it[1] ] }
+    .map{ [ it[0], 'HAPLINK_RAW_HAPLOTYPES', it[1] ] }
     .set{ ch_raw_haplotypes }
 
     HAPLINK_ML_HAPLOTYPES(
@@ -58,7 +58,7 @@ workflow {
     )
     HAPLINK_ML_HAPLOTYPES
         .out
-        .map{ [ it[0], 'ml', it[1] ] }
+        .map{ [ it[0], 'HAPLINK_ML_HAPLOTYPES', it[1] ] }
         .set{ ch_ml_haplotypes }
 
     ch_raw_haplotypes
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index bd09d66..109b92f 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -11,7 +11,7 @@ process HAPLINK_SEQUENCES {
     output:
     tuple val(prefix), val(method), path("*.fasta")
 
-    publishDir "results/${method}-haplotypes", mode: 'copy'
+    publishDir "results/${method}", mode: 'copy'
 
     script:
     """