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Make lineages_topology output optional in FREYJA_UPDATE #11124

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Make lineages_topology output optional in FREYJA_UPDATE #11124

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83099a5
Make lineages_topology output optional
sam-baird Apr 6, 2026
4734753
Merge branch 'master' into freyja-optional-lineagesyml
famosab Apr 8, 2026
dbe3d5d
Merge branch 'master' into freyja-optional-lineagesyml
famosab Apr 8, 2026
2d8208b
Merge branch 'master' into freyja-optional-lineagesyml
famosab Apr 9, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/freyja/update/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process FREYJA_UPDATE {

output:
path "${db_name}/*barcodes.*" , emit: barcodes
path "${db_name}/*lineages.yml" , emit: lineages_topology
path "${db_name}/*lineages.yml" , emit: lineages_topology, optional: true
path "${db_name}/*pathogen_config.yml" , emit: config
path "${db_name}/*curated_lineages.json" , emit: lineages_meta, optional: true
tuple val("${task.process}"), val('freyja'), eval("freyja --version | sed 's/.* //'"), topic: versions, emit: versions_freyja
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28 changes: 28 additions & 0 deletions modules/nf-core/freyja/update/tests/main.nf.test
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Expand Up @@ -67,6 +67,34 @@ nextflow_process {
}
}

test("RSVa - value db name - no lineages_topology ") {

when {
params {
freyja_update_args = "--pathogen RSVa"
}

process {
"""
input[0] = "test_db"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.config.get(0)).text.contains("RSVa") },
{ assert process.out.lineages_topology == [] },
{ assert snapshot(
file(process.out.barcodes.get(0)).name,
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
}
}

test("SARS-cov-2 - value db name - stub ") {
options "-stub"

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31 changes: 25 additions & 6 deletions modules/nf-core/freyja/update/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,11 @@
]
}
],
"timestamp": "2026-02-19T09:58:44.069216",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2026-02-19T09:58:44.069216"
}
},
"sarscov2 - value db name ": {
"content": [
Expand All @@ -44,11 +44,30 @@
]
}
],
"timestamp": "2026-02-19T09:58:31.628204",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2026-02-19T09:58:31.628204"
}
},
"RSVa - value db name - no lineages_topology ": {
"content": [
"RSVa_barcodes.csv",
{
"versions_freyja": [
[
"FREYJA_UPDATE",
"freyja",
"2.0.3"
]
]
}
],
"timestamp": "2026-04-03T23:23:55.517856659",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"MPX - value db name ": {
"content": [
Expand All @@ -64,10 +83,10 @@
]
}
],
"timestamp": "2026-02-19T09:49:00.685131",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2026-02-19T09:49:00.685131"
}
}
}
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