From 5162f649d876d61dc18132feb16e9fb89184839f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:26:25 -0500
Subject: [PATCH] refactor: Move HAPLINK_SEQUENCES module to its own file

---
 main.nf                           | 25 +------------------------
 modules/haplink/sequences/main.nf | 23 +++++++++++++++++++++++
 2 files changed, 24 insertions(+), 24 deletions(-)
 create mode 100644 modules/haplink/sequences/main.nf

diff --git a/main.nf b/main.nf
index f6fbf59..8bc7a7f 100755
--- a/main.nf
+++ b/main.nf
@@ -3,6 +3,7 @@
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
+include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
@@ -74,27 +75,3 @@ workflow {
         ch_reference
     )
 }
-
-process HAPLINK_SEQUENCES {
-    cpus 1
-    memory '6.GB'
-
-    input:
-    tuple val(prefix), val(method), path(yaml)
-    path reference
-
-    output:
-    tuple val(prefix), val(method), path("*.fasta")
-
-    publishDir "results/${method}-haplotypes", mode: 'copy'
-
-    script:
-    """
-    export JULIA_NUM_THREADS=${task.cpus}
-    haplink sequences \\
-            "${reference}" \\
-            "${yaml}" \\
-            --prefix "${prefix}" \\
-        > "${prefix}.fasta"
-    """
-}
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
new file mode 100644
index 0000000..46610e8
--- /dev/null
+++ b/modules/haplink/sequences/main.nf
@@ -0,0 +1,23 @@
+process HAPLINK_SEQUENCES {
+    cpus 1
+    memory '6.GB'
+
+    input:
+    tuple val(prefix), val(method), path(yaml)
+    path reference
+
+    output:
+    tuple val(prefix), val(method), path("*.fasta")
+
+    publishDir "results/${method}-haplotypes", mode: 'copy'
+
+    script:
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink sequences \\
+            "${reference}" \\
+            "${yaml}" \\
+            --prefix "${prefix}" \\
+        > "${prefix}.fasta"
+    """
+}