From 286971d51263e6c7385f925b50547b1b7f4c71fb Mon Sep 17 00:00:00 2001
From: hoelzer <hoelzer.martin@gmail.com>
Date: Fri, 15 Mar 2024 09:11:33 +0100
Subject: [PATCH] add sc2 autodownload

---
 modules/prepare_contamination.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/prepare_contamination.nf b/modules/prepare_contamination.nf
index 51476e5..678635e 100644
--- a/modules/prepare_contamination.nf
+++ b/modules/prepare_contamination.nf
@@ -35,6 +35,10 @@ process download_host {
     eco)
       wget ftp://ftp.ensemblgenomes.org/pub/release-45/bacteria//fasta/bacteria_90_collection/escherichia_coli_k_12/dna/Escherichia_coli_k_12.ASM80076v1.dna.toplevel.fa.gz -O host-temp.fa.gz
       ;;
+    sc2)
+      wget "https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3?download=true" -O host-temp.fa
+      gzip host-temp.fa
+      ;;
     *)
       echo "Unknown host ($host)."
       ;;