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Upload sequences for all segments to S3 #183

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merged 2 commits into from
Oct 15, 2024
Merged

Upload sequences for all segments to S3 #183

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e4d886e
Upload sequences for all segments to S3
huddlej Oct 14, 2024
8e8be63
Remove Yam from the list of lineages to upload
huddlej Oct 14, 2024
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40 changes: 6 additions & 34 deletions profiles/upload.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,12 @@ lat-longs: "config/lat_longs.tsv"
segments:
- ha
- na
- pb2
- pb1
- pa
- np
- mp
- ns

tree:
method: iqtree
Expand Down Expand Up @@ -206,37 +212,3 @@ builds:
- name: vidrl_ferret_egg_hi
data: "data/vic/vidrl_ferret_egg_hi_titers.tsv"
subsamples: *representative-subsampling-scheme
yam_2y:
lineage: yam
reference: "config/yam/{segment}/reference.fasta"
annotation: "config/yam/{segment}/genemap.gff"
tree_exclude_sites: "config/yam/{segment}/exclude-sites.txt"
clades: "config/yam/ha/clades.tsv"
auspice_config: "config/yam/auspice_config.json"
min_date: "2Y"
reference_min_date: "8Y"
include: "config/yam/reference_strains.txt"
exclude: "config/yam/outliers.txt"
vaccines: "config/yam/vaccine.json"
titer_collections:
- name: who_ferret_cell_hi
data: "data/yam/who_ferret_cell_hi_titers.tsv"
- name: who_ferret_egg_hi
data: "data/yam/who_ferret_egg_hi_titers.tsv"
- name: cdc_ferret_cell_hi
data: "data/yam/cdc_ferret_cell_hi_titers.tsv"
- name: cdc_ferret_egg_hi
data: "data/yam/cdc_ferret_egg_hi_titers.tsv"
- name: crick_ferret_cell_hi
data: "data/yam/crick_ferret_cell_hi_titers.tsv"
- name: crick_ferret_egg_hi
data: "data/yam/crick_ferret_egg_hi_titers.tsv"
- name: niid_ferret_cell_hi
data: "data/yam/niid_ferret_cell_hi_titers.tsv"
- name: niid_ferret_egg_hi
data: "data/yam/niid_ferret_egg_hi_titers.tsv"
- name: vidrl_ferret_cell_hi
data: "data/yam/vidrl_ferret_cell_hi_titers.tsv"
- name: vidrl_ferret_egg_hi
data: "data/yam/vidrl_ferret_egg_hi_titers.tsv"
subsamples: *representative-subsampling-scheme