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Add configurable staged input files for the phylogenetic github action #50

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May 20, 2024
Merged

Add configurable staged input files for the phylogenetic github action #50

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4 changes: 2 additions & 2 deletions .github/workflows/phylogenetic.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,13 +32,13 @@ on:
type: string
sequences_url:
description: |
URL for a sequences.fasta.zst file.
URL for sequences_{serotype}.fasta.zst files where {serotype} will be replaced by all, denv1 to denv4.
If not provided, will use default sequences_url from phylogenetic/config/config_dengue.yaml
required: false
type: string
metadata_url:
description: |
URL for a metadata.tsv.zst file.
URL for metadata_{serotype}.tsv.zst files where {serotype} will be replaced by all, denv1 to denv4.
If not provided, will use default metadata_url from phylogenetic/config/config_dengue.yaml
required: false
type: string
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6 changes: 6 additions & 0 deletions phylogenetic/config/config_dengue.yaml
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@@ -1,3 +1,9 @@
# Sequences must be FASTA and metadata must be TSV
# Both files must be zstd compressed
# Both files must have a {serotype} expandable field to be replaced by all, denv1-denv4
sequences_url: "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst"
metadata_url: "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"

strain_id_field: "genbank_accession"
display_strain_field: "strain"

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4 changes: 2 additions & 2 deletions phylogenetic/rules/prepare_sequences.smk
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Expand Up @@ -21,8 +21,8 @@ rule download:
metadata = "data/metadata_{serotype}.tsv.zst"

params:
sequences_url = "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst",
metadata_url = "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"
sequences_url = config["sequences_url"],
metadata_url = config["metadata_url"],
shell:
"""
curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}
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