Merge pull request #87 from rki-mf1/add-sc2

add sc2 autodownload
rki-mf1 · Mar 15, 2024 · 711532e · 711532e
2 parents 5376a82 + 286971d
commit 711532e
Showing 1 changed file with 4 additions and 0 deletions.
diff --git 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)."
       ;;