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Use gisaid_epi_isl in workflows #180

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merged 3 commits into from
Oct 16, 2024
Merged

Use gisaid_epi_isl in workflows #180

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ae1c054
nextclade: Update workflow to use `gisaid_epi_isl`
joverlee521 Sep 10, 2024
d5e1e56
Update Auspice config JSONs to include `gisaid_epi_isl`
joverlee521 Sep 10, 2024
6ddfdba
Move `accession_ha` and `accession_na` to metadata columns
joverlee521 Sep 10, 2024
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15 changes: 5 additions & 10 deletions config/h1n1pdm/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -87,16 +87,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -164,5 +154,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/h1n1pdm/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -162,16 +162,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -239,5 +229,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/h1n1pdm/na/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -127,16 +127,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -204,5 +194,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/h3n2/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -97,16 +97,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -174,5 +164,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
5 changes: 5 additions & 0 deletions config/h3n2/auspice_config_fitness.json
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Original file line number Diff line number Diff line change
Expand Up @@ -152,5 +152,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/h3n2/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -140,16 +140,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -217,5 +207,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/h3n2/na/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -112,16 +112,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -189,5 +179,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/vic/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -72,16 +72,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -149,5 +139,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/vic/ha/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -119,16 +119,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -196,5 +186,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/vic/na/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -112,16 +112,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -189,5 +179,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
15 changes: 5 additions & 10 deletions config/yam/auspice_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -67,16 +67,6 @@
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
Expand Down Expand Up @@ -127,5 +117,10 @@
"map",
"entropy",
"frequencies"
],
"metadata_columns": [
"gisaid_epi_isl",
"accession_ha",
"accession_na"
]
}
4 changes: 2 additions & 2 deletions nextclade/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -410,8 +410,8 @@ rule export:
output:
auspice_json="build/{lineage}/{segment}/{reference}/auspice.json",
params:
fields="strain region country date isolate_id accession_{segment}",
select_fields = ','.join(["strain", "region", "country", "date", "isolate_id", "accession_{segment}"]),
fields="strain region country date gisaid_epi_isl accession_{segment}",
select_fields = ','.join(["strain", "region", "country", "date", "gisaid_epi_isl", "accession_{segment}"]),
date=datetime.datetime.utcnow().strftime("%Y-%m-%d"),
shell:
"""
Expand Down