feat: Add SHORAH_AMPLICON process

main.nf

@@ -142,6 +142,29 @@ process MINIMAP2 {
     """
 }
 
+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 HAPLINK_VARIANTS {
     cpus 2
     memory '12.GB'