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Update salsa2: topic versions, stub block, sanitizeOutput #11445

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Update salsa2: topic versions, stub block, sanitizeOutput #11445

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21b62dc
feat(salsa2): migrate to topic: versions, add stub block, sanitizeOut…
HReed1 Apr 30, 2026
4c93d95
Standardize version emission and restore EDAM comments
HReed1 May 1, 2026
25b9f8b
fix(salsa2): rename emit to versions_salsa2, update snapshots
HReed1 May 1, 2026
dcf3799
Merge branch 'master' into stub-topics-salsa2
HReed1 May 3, 2026
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13 changes: 7 additions & 6 deletions modules/nf-core/salsa2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ process SALSA2 {
tuple val(meta), path("*_scaffolds_FINAL.fasta") , emit: fasta
tuple val(meta), path("*_scaffolds_FINAL.agp") , emit: agp
tuple val(meta), path("*/*scaffolds_FINAL.original-coordinates.agp"), emit: agp_original_coordinates, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('salsa2'), eval("echo 2.3"), topic: versions, emit: versions_salsa2
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@SPPearce SPPearce May 1, 2026

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Suggested change
tuple val("${task.process}"), val('salsa2'), eval("echo 2.3"), topic: versions, emit: versions_salsa2
tuple val("${task.process}"), val('salsa2'), val("2.3"), topic: versions, emit: versions_salsa2


when:
task.ext.when == null || task.ext.when
Expand All @@ -30,7 +30,6 @@ process SALSA2 {
def gfa_opt = gfa ? "--gfa $gfa" : ""
def dup_opt = dup ? "--dup $dup" : ""
def filter = filter_bed ? "--filter $filter_bed" : ""
def VERSION = '2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
run_pipeline.py \\
$args \\
Expand All @@ -43,10 +42,12 @@ process SALSA2 {

mv */scaffolds_FINAL.fasta ${prefix}_scaffolds_FINAL.fasta
mv */scaffolds_FINAL.agp ${prefix}_scaffolds_FINAL.agp
"""

cat <<-END_VERSIONS > versions.yml
"${task.process}":
SALSA2: $VERSION
END_VERSIONS
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_scaffolds_FINAL.fasta
touch ${prefix}_scaffolds_FINAL.agp
"""
}
41 changes: 29 additions & 12 deletions modules/nf-core/salsa2/meta.yml
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Expand Up @@ -14,7 +14,8 @@ tools:
documentation: "https://github.com/marbl/SALSA"
tool_dev_url: "https://github.com/marbl/SALSA"
doi: "10.1186/s12864-017-3879-z"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- - meta:
Expand All @@ -29,7 +30,8 @@ input:
ontologies: []
- index:
type: file
description: Fasta index file of assembly containing the length of contigs.
description: Fasta index file of assembly containing the length of
contigs.
pattern: "*.{fa.fai, fasta.fai}"
ontologies: []
- bed:
Expand Down Expand Up @@ -70,8 +72,8 @@ output:
e.g. [ id:'test', single_end:false ]
- "*_scaffolds_FINAL.agp":
type: file
description: AGP style output for the scaffolds describing the assignment,
orientation and ordering of contigs along the scaffolds
description: AGP style output for the scaffolds describing the
assignment, orientation and ordering of contigs along the scaffolds
pattern: "*_scaffolds_FINAL.agp"
ontologies: []
agp_original_coordinates:
Expand All @@ -82,17 +84,32 @@ output:
e.g. [ id:'test', single_end:false ]
- "*/*scaffolds_FINAL.original-coordinates.agp":
type: file
description: Secondary output AGP file with names and coordinates matching
the original input assembly (optional)
description: Secondary output AGP file with names and coordinates
matching the original input assembly (optional)
pattern: "*scaffolds_FINAL.original-coordinates.agp"
ontologies: []

versions_salsa2:
- - ${task.process}:
type: string
description: The name of the process
- salsa2:
type: string
description: The name of the tool
- echo 2.3:
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- salsa2:
type: string
description: The name of the tool
- echo 2.3:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@scorreard"
maintainers:
Expand Down
34 changes: 31 additions & 3 deletions modules/nf-core/salsa2/tests/main.nf.test
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Expand Up @@ -30,9 +30,37 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out.fasta).match("fasta") },
{ assert snapshot(process.out.agp).match("agp") },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}

test("Single-Read - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end: false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[1] = [
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
]
input[2] = []
input[3] = []
input[4] = []
"""
}
}

then {
assertAll (
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
98 changes: 70 additions & 28 deletions modules/nf-core/salsa2/tests/main.nf.test.snap
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@@ -1,38 +1,80 @@
{
"versions": {
"Single-Read - stub": {
"content": [
[
"versions.yml:md5,5985e59c635903ae7725afa4f5368de7"
]
],
"timestamp": "2024-05-22T19:35:47.254995"
},
"agp": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.agp:md5,03fe8c559b80730aab465697a6b0e01c"
{
"agp": [
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"agp_original_coordinates": [

],
"fasta": [
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_salsa2": [
[
"SALSA2",
"salsa2",
"2.3"
]
]
]
}
],
"timestamp": "2024-05-22T19:34:18.646515"
"timestamp": "2026-04-30T17:20:13.326132",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"fasta": {
"Single-Read": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.fasta:md5,32c805e9e447ad47d6437e10f91bd5bf"
{
"agp": [
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.agp:md5,03fe8c559b80730aab465697a6b0e01c"
]
],
"agp_original_coordinates": [

],
"fasta": [
[
{
"id": "test",
"single_end": false
},
"test_scaffolds_FINAL.fasta:md5,32c805e9e447ad47d6437e10f91bd5bf"
]
],
"versions_salsa2": [
[
"SALSA2",
"salsa2",
"2.3"
]
]
]
}
],
"timestamp": "2024-05-22T19:35:47.240011"
"timestamp": "2026-04-30T17:19:21.703989",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
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