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Move the NCBI field map to config #219

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Merged
j23414 merged 1 commit into from
Nov 2, 2023
Merged

Move the NCBI field map to config #219

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2 changes: 2 additions & 0 deletions ingest/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
sources: ['genbank']
# Pathogen NCBI Taxonomy ID
ncbi_taxon_id: '10244'
# Renames the NCBI dataset headers
ncbi_field_map: 'source-data/ncbi-dataset-field-map.tsv'

# Params for the transform rule
transform:
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2 changes: 1 addition & 1 deletion ingest/workflow/snakemake_rules/fetch_sequences.smk
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Expand Up @@ -80,7 +80,7 @@ rule format_ncbi_dataset_report:
# The only fields we do not have equivalents for are "title" and "publications"
input:
dataset_package="data/ncbi_dataset.zip",
ncbi_field_map="source-data/ncbi-dataset-field-map.tsv",
ncbi_field_map=config["ncbi_field_map"],
output:
ncbi_dataset_tsv=temp("data/ncbi_dataset_report.tsv"),
params:
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