Add back nextstrain-specific files in default params.yaml until workflow is fixed
@@ -20,13 +20,21 @@ files:
include: "defaults/include.txt"
exclude: "defaults/exclude.txt"
reference: "defaults/reference_seq.gb"
- outgroup: "defaults/outgroup.fasta" # is this arg still used? file doesn't exist in default repo
+ outgroup: "defaults/outgroup.fasta" # is this arg still used? file doesn't exist in gh repo
ordering: "defaults/color_ordering.tsv"
color_schemes: "defaults/color_schemes.tsv"
auspice_config: "defaults/auspice_config.json"
lat_longs: "defaults/lat_longs.tsv"
description: "defaults/description.md"
clades: "defaults/clades.tsv"
+ legacy_clades: "nextstrain_profiles/nextstrain/legacy_clades.tsv" # dependency should be moved --> nextstrain_profiles specific
+ auspice_config_gisaid: "nextstrain_profiles/nextstrain/legacy_clades.tsv" # dependency should be moved --> nextstrain_profiles specific
+ auspice_config_zh: "nextstrain_profiles/nextstrain/auspice_config_zh" # dependency should be moved --> nextstrain_profiles specific
+ description_zh: "nextstrain_profiles/nextstrain/description_zh.md" # dependency should be moved --> nextstrain_profiles specific
+
+s3_staging_url: s3://nextstrain-staging # dependency should be moved --> nextstrain_profiles specific
+slack_token: ~ # dependency should be moved --> nextstrain_profiles specific
+slack_channel: "#ncov-gisaid-updates" # dependency should be moved --> nextstrain_profiles specific
# Filter settings
filter:
