From 18875ae1a63de8d09d8ca9db7669a38417ced0f9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 15:34:27 -0500
Subject: [PATCH] refactor: Move EFETCH module to its own file

---
 main.nf                | 22 +---------------------
 modules/efetch/main.nf | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 21 deletions(-)
 create mode 100644 modules/efetch/main.nf

diff --git a/main.nf b/main.nf
index 69acadb..3d4bf6a 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { EFETCH } from './modules/efetch'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { VIQUAS } from './modules/viquas'
 
@@ -68,27 +69,6 @@ workflow {
     )
 }
 
-process EFETCH {
-    cpus 1
-    memory '256.MB'
-    container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
-
-    publishDir "results", mode: 'copy'
-
-    output:
-    path 'idv4.fasta'
-
-    script:
-    """
-    esearch \\
-            -db nucleotide \\
-            -query "NC_036618.1" \\
-        | efetch \\
-            -format fasta \\
-        > idv4.fasta
-    """
-}
-
 process NANOFILT {
     cpus 1
     memory '8.GB'
diff --git a/modules/efetch/main.nf b/modules/efetch/main.nf
new file mode 100644
index 0000000..00ec585
--- /dev/null
+++ b/modules/efetch/main.nf
@@ -0,0 +1,20 @@
+process EFETCH {
+    cpus 1
+    memory '256.MB'
+    container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'
+
+    publishDir "results", mode: 'copy'
+
+    output:
+    path 'idv4.fasta'
+
+    script:
+    """
+    esearch \\
+            -db nucleotide \\
+            -query "NC_036618.1" \\
+        | efetch \\
+            -format fasta \\
+        > idv4.fasta
+    """
+}