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add seq_type to anarcii module #12813

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a6f2c74
add seq_type to anarcii module
mapo9 Aug 26, 2026
385d1a6
add missing snapshot test and update snapshot
mapo9 Aug 26, 2026
1f8f413
snapshot stable anarcii fields instead of the output md5
mapo9 Aug 26, 2026
22a5939
Merge branch 'master' into anarcii_seqtype
mapo9 Aug 26, 2026
4f0af78
allow singularity_pull_docker_container override in anarcii container
mapo9 Aug 27, 2026
65a281d
Merge branch 'master' into anarcii_seqtype
mapo9 Aug 27, 2026
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4 changes: 3 additions & 1 deletion modules/nf-core/anarcii/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,13 @@ process ANARCII {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine in ['singularity', 'apptainer']
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c5/c56cb3320588978063f0893876f4f2b6f088dadc75628f60a746ee54e72350a6/data'
: 'community.wave.seqera.io/library/python_pip_anarcii:4e5c3ffabd22d3fc'}"

input:
tuple val(meta), path(fasta)
val seq_type

output:
tuple val(meta), path("*.csv"), emit: anarcii
Expand All @@ -22,6 +23,7 @@ process ANARCII {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
anarcii \\
-t ${seq_type} \\
${args}\\
-o ${prefix}.csv \\
${fasta}
Expand Down
5 changes: 5 additions & 0 deletions modules/nf-core/anarcii/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,11 @@ input:
pattern: "*.fasta"
ontologies:
- edam: http://edamontology.org/format_1929
- seq_type:
type: string
description: |
Receptor type to number, passed to ANARCII's `-t` flag. Selects the model used for alignment.
pattern: "antibody|tcr|vnar|vhh|shark|unknown"
output:
anarcii:
- - meta:
Expand Down
13 changes: 13 additions & 0 deletions modules/nf-core/anarcii/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ nextflow_process {
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/anarcii/anarcii_vdjdb.fasta', checkIfExists: true),
]
input[1] = 'tcr'
"""
}
}
Expand All @@ -30,6 +31,17 @@ nextflow_process {
assert "Score" in anarciiResults.columnNames
assert "Query start" in anarciiResults.columnNames
assert "Query end" in anarciiResults.columnNames
// A mismatched seq_type leaves sequences unnumbered as chain "F" instead of failing
assert anarciiResults.columns["Chain"].every { it in ["A", "B"] }
// Score drifts with thread count, so the file md5 is not portable across machines
assert snapshot(
anarciiResults.columnNames.sort(),
anarciiResults.columns["Name"],
anarciiResults.columns["Chain"],
anarciiResults.columns["Query start"],
anarciiResults.columns["Query end"],
process.out.versions_anarcii
).match()
}
}

Expand All @@ -44,6 +56,7 @@ nextflow_process {
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/anarcii/anarcii_vdjdb.fasta', checkIfExists: true),
]
input[1] = 'tcr'
"""
}
}
Expand Down
203 changes: 203 additions & 0 deletions modules/nf-core/anarcii/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,207 @@
{
"human - fasta": {
"content": [
[
"1",
"10",
"100",
"101",
"102",
"103",
"104",
"105",
"106",
"107",
"108",
"109",
"11",
"110",
"111",
"111A",
"111B",
"112",
"112A",
"112B",
"113",
"114",
"115",
"116",
"117",
"118",
"119",
"12",
"120",
"121",
"122",
"123",
"124",
"125",
"126",
"127",
"128",
"13",
"14",
"15",
"16",
"17",
"18",
"19",
"2",
"20",
"21",
"22",
"23",
"24",
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"3",
"30",
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"39",
"4",
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"5",
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"53",
"54",
"55",
"56",
"57",
"58",
"59",
"6",
"60",
"61",
"62",
"63",
"64",
"65",
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"68",
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"7",
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"8",
"80",
"81",
"82",
"83",
"84",
"85",
"86",
"87",
"88",
"89",
"9",
"90",
"91",
"92",
"93",
"94",
"95",
"96",
"97",
"98",
"99",
"Chain",
"Name",
"Query end",
"Query start",
"Score"
],
[
"298|TRA",
"298|TRB",
"299|TRA",
"299|TRB",
"300|TRA",
"300|TRB",
"301|TRA",
"301|TRB",
"302|TRA",
"302|TRB"
],
[
"A",
"B",
"A",
"B",
"A",
"B",
"A",
"B",
"A",
"B"
],
[
20,
19,
19,
19,
20,
19,
18,
19,
18,
19
],
[
133,
133,
132,
131,
135,
137,
130,
130,
130,
133
],
[
[
"ANARCII",
"anarcii",
"2.0.5"
]
]
],
"timestamp": "2026-08-26T11:14:14.316916324",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"human - fasta - stub": {
"content": [
{
Expand Down