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Remove unused variables and refactor GENE_LIST #437

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Feb 22, 2024
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9 changes: 6 additions & 3 deletions Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,12 @@ import os
# Snakemake 7.7.0 introduced `retries` directive used in fetch_sequences
min_version("7.7.0")

GENES = "E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S"
GENES_SPACE_DELIMITED = GENES.replace(",", " ")
GENE_LIST = GENES.split(",")
# Hardcoded gene list used to create the DAG for both nextclade.smk and upload.smk
# It does _not_ need to be supplied to the `nextclade run` invocations because
# it matches the genes listed in the SARS-CoV-2 Nextclade dataset genome_annotations.gff
# https://github.com/nextstrain/nextclade_data/blob/244058e7d599a8295d748b12cffdd25cec6d3e7b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/genome_annotation.gff3
# - Jover, 21 Feb 2024
GENE_LIST = ['E', 'M', 'N', 'ORF1a', 'ORF1b', 'ORF3a', 'ORF6', 'ORF7a', 'ORF7b', 'ORF8', 'ORF9b', 'S']

#################################################################
####################### general setup ###########################
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