refactor: Make reference genome an input for EFETCH

main.nf

@@ -11,7 +11,7 @@ workflow {
         .map { file -> tuple(file.simpleName, file) }
         .set { ch_input }
 
-    EFETCH()
+    EFETCH('NC_036618.1')
     EFETCH
         .out
         .set { ch_reference }

modules/efetch/main.nf

@@ -3,6 +3,9 @@ process EFETCH {
 
     container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
 
+    input:
+    val(genome)
+
     publishDir "results", mode: 'copy'
 
     output:
@@ -12,7 +15,7 @@ process EFETCH {
     """
     esearch \\
             -db nucleotide \\
-            -query "NC_036618.1" \\
+            -query "${genome}" \\
         | efetch \\
             -format fasta \\
         > idv4.fasta