Remove unused variables and refactor GENE_LIST
#437
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Noted in previous PRs that that the `GENES` and `GENES_SPACE_DELIMITED` variables are not needed¹ or used in the workflow,² so refactor the `GENE_LIST` to be a hardcoded list of genes. If we want to ensure that we do not miss any genes from the Nextclade dataset, we could parse out the gene names from the dataset's genome_annotation.gff file. However, I think that will over-complicate the Snakemake workflow so I'm leaving the hardcoded list. ¹ #372 (comment) ² #435 (comment)
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Tested locally by running the debug config All translation_*.fasta.zst files have been uploaded to |
This was referenced Feb 21, 2024
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Noted in previous PRs that that the
GENESandGENES_SPACE_DELIMITEDvariables are not needed¹ or used in the workflow,² so refactor theGENE_LISTto be a hardcoded list of genes.If we want to ensure that we do not miss any genes from the Nextclade dataset, we could parse out the gene names from the dataset's genome_annotation.gff file. However, I think that will over-complicate the Snakemake workflow so I'm leaving the hardcoded list.
¹ #372 (comment)
² #435 (comment)
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