From dbea6fb30a105b134a75874606b7a2cb4247cc5e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:09:21 -0500
Subject: [PATCH] refactor: Move SHORAH_AMPLICON to its own file

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

diff --git a/main.nf b/main.nf
index b80f998..82a0fbf 100755
--- a/main.nf
+++ b/main.nf
@@ -4,6 +4,7 @@ include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { MINIMAP2 } from './modules/minimap2'
 include { NANOFILT } form './modules/nanofilt'
+include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -71,29 +72,6 @@ workflow {
     )
 }
 
-process SHORAH_AMPLICON {
-    label 'process_high'
-    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
-
-    input:
-    tuple val(prefix), path(bam)
-    path(reference)
-
-    output:
-    tuple val(prefix), path("*.vcf")
-    tuple val(prefix), path("*support.fas")
-
-    publishDir "results/shorah-amplicon", mode: 'copy'
-
-    script:
-    """
-    shorah amplicon \\
-        -t ${task.cpus} \\
-        -f ${reference} \\
-        -b ${bam} \\
-    """
-}
-
 process SHORAH_SHOTGUN {
     label 'process_high'
     container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
diff --git a/modules/shorah/amplicon/main.nf b/modules/shorah/amplicon/main.nf
new file mode 100644
index 0000000..c15cd43
--- /dev/null
+++ b/modules/shorah/amplicon/main.nf
@@ -0,0 +1,22 @@
+process SHORAH_AMPLICON {
+    label 'process_high'
+    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.vcf")
+    tuple val(prefix), path("*support.fas")
+
+    publishDir "results/shorah-amplicon", mode: 'copy'
+
+    script:
+    """
+    shorah amplicon \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}