Add gisaid rule to Snakefile
@@ -420,3 +420,19 @@ rule clean:
"auspice"
shell:
"rm -rfv {params}"
+
+rule gisaid:
+ message: "Normalizing GISAID download"
+ input:
+ gisaid_fasta = "data/gisaid_cov2020_sequences.fasta"
+ output:
+ sequences = "data/sequences.fasta"
+ params:
+ min_length = 15000
+ shell:
+ """
+ if [[ ! -f "data/sequences.fasta" && -f "data/gisaid_cov2020_sequences.fasta" ]]
+ then
+ scripts/normalize_gisaid_fasta.sh data/gisaid_cov2020_sequences.fasta data/sequences.fasta {params.min_length}
+ fi
+ """
