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Ingest nextclade updates #54

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merged 3 commits into from
Jul 16, 2024
Merged

Ingest nextclade updates #54

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0446aa2
ingest/nextclade_config: Fix file path for field_map
joverlee521 Jul 13, 2024
63b2fe1
ingest/nextclade_field_map: Remove `lineage`
joverlee521 Jul 12, 2024
b6f07a6
ingest/nextclade: Update to Nextclade v3
joverlee521 Jul 12, 2024
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2 changes: 1 addition & 1 deletion ingest/defaults/nextclade_config.yaml
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Expand Up @@ -6,7 +6,7 @@ nextclade:
dataset_name: ""
# Path to the mapping for renaming Nextclade output columns
# The path should be relative to the ingest directory
field_map: "config/nextclade_field_map.tsv"
field_map: "defaults/nextclade_field_map.tsv"
# This is the ID field you would use to match the Nextclade output with the record metadata.
# This should be the new name that you have defined in your field map.
id_field: "seqName"
1 change: 0 additions & 1 deletion ingest/defaults/nextclade_field_map.tsv
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Expand Up @@ -5,7 +5,6 @@
# columns would be useful for your downstream phylogenetic analysis.
seqName seqName
clade clade
lineage lineage
coverage coverage
totalMissing missing_data
totalSubstitutions divergence
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6 changes: 3 additions & 3 deletions ingest/rules/nextclade.smk
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Expand Up @@ -29,7 +29,7 @@ rule get_nextclade_dataset:
dataset_name=DATASET_NAME
shell:
"""
nextclade2 dataset get \
nextclade3 dataset get \
--name={params.dataset_name:q} \
--output-zip={output.dataset} \
--verbose
Expand All @@ -47,10 +47,10 @@ rule run_nextclade:
params:
# The lambda is used to deactivate automatic wildcard expansion.
# https://github.com/snakemake/snakemake/blob/384d0066c512b0429719085f2cf886fdb97fd80a/snakemake/rules.py#L997-L1000
translations=lambda w: "results/translations/{gene}.fasta",
translations=lambda w: "results/translations/{cds}.fasta",
shell:
"""
nextclade2 run \
nextclade3 run \
{input.sequences} \
--input-dataset {input.dataset} \
--output-tsv {output.nextclade} \
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