From 2829d515336a3a96300b11f1ad32020506a9a3ba Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:21:26 -0500
Subject: [PATCH] refactor: Move HAPLINK_VARIANTS module to its own folder

---
 main.nf                          | 24 +-----------------------
 modules/haplink/variants/main.nf | 22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 23 deletions(-)
 create mode 100644 modules/haplink/variants/main.nf

diff --git a/main.nf b/main.nf
index 58335df..69acadb 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -195,29 +196,6 @@ process SHORAH_SHOTGUN {
     """
 }
 
-process HAPLINK_VARIANTS {
-    cpus 2
-    memory '12.GB'
-
-    input:
-    tuple val(prefix), path(bam), path(bai)
-    path reference
-
-    output:
-    tuple val(prefix), path("*.vcf")
-
-    publishDir "results", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink variants \\
-            "${reference}" \\
-            "${bam}" \\
-        > "${prefix}.vcf"
-    """
-}
-
 process HAPLINK_RAW_HAPLOTYPES {
     cpus 2
     memory '12.GB'
diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
new file mode 100644
index 0000000..8e2c48f
--- /dev/null
+++ b/modules/haplink/variants/main.nf
@@ -0,0 +1,22 @@
+process HAPLINK_VARIANTS {
+    cpus 2
+    memory '12.GB'
+
+    input:
+    tuple val(prefix), path(bam), path(bai)
+    path reference
+
+    output:
+    tuple val(prefix), path("*.vcf")
+
+    publishDir "results", mode: 'copy'
+
+    script:
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink variants \\
+            "${reference}" \\
+            "${bam}" \\
+        > "${prefix}.vcf"
+    """
+}