refactor: Move SHORAH_SHOTGUN to its own file

main.nf

@@ -5,6 +5,7 @@ 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 { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
 include { VIQUAS } from './modules/viquas'
 
 workflow {
@@ -72,29 +73,6 @@ workflow {
     )
 }
 
-process SHORAH_SHOTGUN {
-    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-shotgun", mode: 'copy'
-
-    script:
-    """
-    shorah shotgun \\
-        -t ${task.cpus} \\
-        -f ${reference} \\
-        -b ${bam} \\
-    """
-}
-
 process HAPLINK_RAW_HAPLOTYPES {
     cpus 2
     memory '12.GB'

modules/shorah/shotgun/main.nf

@@ -0,0 +1,22 @@
+process SHORAH_SHOTGUN {
+    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-shotgun", mode: 'copy'
+
+    script:
+    """
+    shorah shotgun \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}