From a9aa590f007574090208bc3b946276c88c94acc8 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:05:02 -0500
Subject: [PATCH] refactor: Move MINIMAP2 module to separate file

---
 main.nf                  | 34 +---------------------------------
 modules/minimap2/main.nf | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 33 deletions(-)
 create mode 100644 modules/minimap2/main.nf

diff --git a/main.nf b/main.nf
index 3d938fa..b80f998 100755
--- a/main.nf
+++ b/main.nf
@@ -2,6 +2,7 @@
 
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
+include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
 include { VIQUAS } from './modules/viquas'
 
@@ -70,39 +71,6 @@ workflow {
     )
 }
 
-process MINIMAP2 {
-    cpus 4
-    memory '8.GB'
-    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
-
-    input:
-    tuple val(prefix), path(reads)
-    path reference
-
-    publishDir "results", mode: 'copy'
-
-    output:
-    tuple val(prefix), path("*.bam"), path("*.bam.bai")
-    script:
-    """
-    minimap2 \\
-            -x map-ont \\
-            --MD \\
-            --eqx \\
-            -t ${task.cpus} \\
-            -a \\
-            "${reference}" \\
-            "${reads}" \\
-    | samtools sort \\
-    | samtools view \\
-            -@ ${task.cpus} \\
-            -b \\
-            -h \\
-            -o "${prefix}.bam"
-    samtools index "${prefix}.bam"
-    """
-}
-
 process SHORAH_AMPLICON {
     label 'process_high'
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
diff --git a/modules/minimap2/main.nf b/modules/minimap2/main.nf
new file mode 100644
index 0000000..610028b
--- /dev/null
+++ b/modules/minimap2/main.nf
@@ -0,0 +1,32 @@
+process MINIMAP2 {
+    cpus 4
+    memory '8.GB'
+    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
+
+    input:
+    tuple val(prefix), path(reads)
+    path reference
+
+    publishDir "results", mode: 'copy'
+
+    output:
+    tuple val(prefix), path("*.bam"), path("*.bam.bai")
+    script:
+    """
+    minimap2 \\
+            -x map-ont \\
+            --MD \\
+            --eqx \\
+            -t ${task.cpus} \\
+            -a \\
+            "${reference}" \\
+            "${reads}" \\
+    | samtools sort \\
+    | samtools view \\
+            -@ ${task.cpus} \\
+            -b \\
+            -h \\
+            -o "${prefix}.bam"
+    samtools index "${prefix}.bam"
+    """
+}