From b1ee784daca2f5a722a85f27d15ebd5c2e642ec9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:38:55 -0500
Subject: [PATCH] refactor: Make reference genome an input for EFETCH

---
 main.nf                | 2 +-
 modules/efetch/main.nf | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 3d4bf6a..54ff5e4 100755
--- a/main.nf
+++ b/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 }
diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
index 2041d45..66272fd 100644
--- a/modules/efetch/main.nf
+++ b/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