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Separate files for RESTRICTED sequences #347

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7629cee
ingest: Add rules to extract "RESTRICTED" data
joverlee521 Nov 14, 2025
7cc5cea
phylo: Update to start from multiple inputs
joverlee521 Nov 14, 2025
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20 changes: 19 additions & 1 deletion ingest/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,25 @@ rule extract_open_data:
augur filter --metadata {input.metadata} \
--sequences {input.sequences} \
--metadata-id-columns PPX_accession \
--exclude-where "dataUseTerms=RESTRICTED" \
--include-where "dataUseTerms=OPEN" \
--output-metadata {output.metadata} \
--output-sequences {output.sequences}
"""


rule extract_restricted_data:
input:
metadata="results/metadata.tsv",
sequences="results/sequences.fasta",
output:
metadata="results/metadata_restricted.tsv",
sequences="results/sequences_restricted.fasta",
shell:
"""
augur filter --metadata {input.metadata} \
--sequences {input.sequences} \
--metadata-id-columns PPX_accession \
--include-where "dataUseTerms=RESTRICTED" \
--output-metadata {output.metadata} \
--output-sequences {output.sequences}
"""
5 changes: 3 additions & 2 deletions ingest/build-configs/nextstrain-automation/config.yaml
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Expand Up @@ -16,14 +16,15 @@ upload:
# to avoid duplicate files with different compressions
files_to_upload:
ppx_with_restricted.ndjson.zst: results/ppx.ndjson.zst
metadata_with_restricted.tsv.zst: results/metadata.tsv
sequences_with_restricted.fasta.zst: results/sequences.fasta

nextclade_with_restricted.tsv.zst: results/nextclade.tsv
alignment_with_restricted.fasta.zst: results/alignment.fasta
translations_with_restricted.zip: results/translations.zip

metadata.tsv.zst: results/metadata_open.tsv
sequences.fasta.zst: results/sequences_open.fasta
metadata_restricted.tsv.zst: results/metadata_restricted.tsv
sequences_restricted.tsv.zst: results/sequences_restricted.fasta

cloudfront_domain: 'data.nextstrain.org'

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9 changes: 6 additions & 3 deletions phylogenetic/defaults/clade-i/config.yaml
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@@ -1,7 +1,10 @@
inputs:
- name: pathoplexus
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_with_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_with_restricted.fasta.zst"
- name: ppx_open
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.zst"
- name: ppx_restricted
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_restricted.fasta.zst"

reference: "defaults/clade-i/reference.fasta"
genome_annotation: "defaults/clade-i/genome_annotation.gff3"
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9 changes: 6 additions & 3 deletions phylogenetic/defaults/hmpxv1/config.yaml
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@@ -1,7 +1,10 @@
inputs:
- name: pathoplexus
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_with_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_with_restricted.fasta.zst"
- name: ppx_open
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.zst"
- name: ppx_restricted
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_restricted.fasta.zst"

reference: "defaults/reference.fasta"
genome_annotation: "defaults/genome_annotation.gff3"
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9 changes: 6 additions & 3 deletions phylogenetic/defaults/hmpxv1_big/config.yaml
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@@ -1,7 +1,10 @@
inputs:
- name: pathoplexus
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_with_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_with_restricted.fasta.zst"
- name: ppx_open
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.zst"
- name: ppx_restricted
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_restricted.fasta.zst"

reference: "defaults/reference.fasta"
genome_annotation: "defaults/genome_annotation.gff3"
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9 changes: 6 additions & 3 deletions phylogenetic/defaults/mpxv/config.yaml
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@@ -1,7 +1,10 @@
inputs:
- name: pathoplexus
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_with_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_with_restricted.fasta.zst"
- name: ppx_open
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.zst"
- name: ppx_restricted
metadata: "https://data.nextstrain.org/files/workflows/mpox/metadata_restricted.tsv.zst"
sequences: "https://data.nextstrain.org/files/workflows/mpox/sequences_restricted.fasta.zst"

auspice_config: "defaults/mpxv/auspice_config.json"
include: "defaults/mpxv/include.txt"
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