Add normalize_gisaid_fasta.sh for issue #53 #59
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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.
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Hi @brianpardy. Thanks so much for this PR. I'm sorry it took so long to review. This works exactly as it should. |
This was referenced Mar 15, 2020
oneillkza
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Add detailed steps for how to obtain and normalize GISAID fasta, as resolved in nextstrain#53 and nextstrain#59 .
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Call as:
scripts/normalize_gisaid_fasta.sh data/gisaid_cov2020_sequences.fasta data/sequences.fasta 15000
Or use params.min_length when calling from Snakefile. Defaults to 15000 if unspecified.
I hope this is proper etiquette to submit this way.