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Move ncbi taxon id to config #217

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Oct 30, 2023
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Move ncbi taxon id to config #217

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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
@@ -1,5 +1,7 @@
# Sources of sequences to include in the ingest run
sources: ['genbank']
# Pathogen NCBI Taxonomy ID
ncbi_taxon_id: '10244'

# Params for the transform rule
transform:
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4 changes: 3 additions & 1 deletion ingest/workflow/snakemake_rules/fetch_sequences.smk
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Expand Up @@ -20,9 +20,11 @@ rule fetch_ncbi_dataset_package:
retries: 5 # Requires snakemake 7.7.0 or later
benchmark:
"benchmarks/fetch_ncbi_dataset_package.txt"
params:
ncbi_taxon_id=config["ncbi_taxon_id"],
shell:
"""
datasets download virus genome taxon 10244 \
datasets download virus genome taxon {params.ncbi_taxon_id} \
--no-progressbar \
--filename {output.dataset_package}
"""
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2 changes: 1 addition & 1 deletion phylogenetic/config/description.md
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Expand Up @@ -18,7 +18,7 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mon

#### Underlying data
We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),
using NCBI Taxonomy ID "10244", as starting point for these analyses.
using an NCBI Taxonomy ID defined in [ingest/config/config.yaml](https://github.com/nextstrain/monkeypox/blob/master/ingest/config/config.yaml), as starting point for these analyses.
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@j23414 j23414 Oct 30, 2023 •
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I realized I could have submitted this as a separate PR. But would this wording be okay, @joverlee521 ?

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LGTM!

Curated sequences and metadata are available as flat files at:
- [data.nextstrain.org/files/workflows/monkeypox/sequences.fasta.xz](https://data.nextstrain.org/files/workflows/monkeypox/sequences.fasta.xz)
- [data.nextstrain.org/files/workflows/monkeypox/metadata.tsv.gz](https://data.nextstrain.org/files/workflows/monkeypox/metadata.tsv.gz)
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