Remove gisaid rule from snakefile
Asking snakemake for "data/sequences.fasta" was throwing an error due to ambiguous DAG. This file can be created by either rule download or rule gisaid. There might be a better solution here, but in order to merge, I'm just going to remove from snakefile.
@@ -420,19 +420,3 @@ 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
- """
