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Add Topic-based tool version capture to Trinity Module #9273

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Merged
merged 7 commits into from
Oct 29, 2025
Merged

Add Topic-based tool version capture to Trinity Module #9273

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f7b6828
add versions topic to trinity module
eit-maxlcummins Oct 28, 2025
87f28c5
add missing test for main.nf.test
eit-maxlcummins Oct 28, 2025
72a677f
simplify string replacement for trinity version eval to remove use of…
eit-maxlcummins Oct 28, 2025
104e308
update meta.yml to capture new version topics change
eit-maxlcummins Oct 28, 2025
2ec0f0f
add new test for aggregating versions via topic
eit-maxlcummins Oct 28, 2025
ff7158e
update snapshot for new tests
eit-maxlcummins Oct 28, 2025
b53a6d8
Update modules/nf-core/trinity/meta.yml
eit-maxlcummins Oct 28, 2025
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12 changes: 1 addition & 11 deletions modules/nf-core/trinity/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process TRINITY {
output:
tuple val(meta), path("*.fa.gz") , emit: transcript_fasta
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'"), topic: versions, emit: versions_trinity

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -61,11 +61,6 @@ process TRINITY {
> ${prefix}.fa.gz

rm ${prefix}_trinity.Trinity.fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trinity: \$(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
END_VERSIONS
"""

stub:
Expand All @@ -74,10 +69,5 @@ process TRINITY {
touch ${prefix}.fa
gzip ${prefix}.fa
touch ${prefix}.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trinity: \$(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
END_VERSIONS
"""
}
28 changes: 21 additions & 7 deletions modules/nf-core/trinity/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -51,13 +51,27 @@ output:
description: Log from trinity
pattern: "*.log"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_trinity:
- - ${task.process}:
type: string
description: The process the versions were collected from
- trinity:
type: string
description: The tool name
- Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//':
type: string
description: The command used to generate the version of the tool
topics:
- versions:
- - process:
type: string
description: The process the versions were collected from
- tool:
type: string
description: The tool name
- version:
type: string
description: The version of the tool
authors:
- "@timslittle"
- "@gallvp"
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/trinity/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ nextflow_process {
{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") },
{ assert snapshot(
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand All @@ -57,7 +57,7 @@ nextflow_process {
{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") },
{ assert snapshot(
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
},
)
Expand Down Expand Up @@ -87,7 +87,7 @@ nextflow_process {
{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") },
{ assert snapshot(
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}

Expand Down Expand Up @@ -116,7 +116,7 @@ nextflow_process {
{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") },
{ assert snapshot(
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match()
}
)
Expand Down Expand Up @@ -144,7 +144,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
)
}
}
Expand Down
113 changes: 51 additions & 62 deletions modules/nf-core/trinity/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,103 +1,92 @@
{
"homo_sapiens-test_rnaseq-paired-multiple": {
"content": [
[
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
]
{
"versions_trinity": [
[
"TRINITY",
"trinity",
"2.15.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
"nextflow": "25.04.6"
},
"timestamp": "2024-11-28T14:08:11.163901364"
"timestamp": "2025-10-28T13:22:02.72961086"
},
"homo_sapiens-test_rnaseq-single": {
"content": [
[
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
]
{
"versions_trinity": [
[
"TRINITY",
"trinity",
"2.15.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
"nextflow": "25.04.6"
},
"timestamp": "2024-11-28T14:07:10.975441404"
"timestamp": "2025-10-28T13:21:13.836913087"
},
"homo_sapiens-test_rnaseq-paired": {
"content": [
[
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
]
{
"versions_trinity": [
[
"TRINITY",
"trinity",
"2.15.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
"nextflow": "25.04.6"
},
"timestamp": "2024-11-28T14:06:36.470824201"
"timestamp": "2025-10-28T13:20:45.185841704"
},
"homo_sapiens-test_rnaseq-single-multiple": {
"content": [
[
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
]
{
"versions_trinity": [
[
"TRINITY",
"trinity",
"2.15.2"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
"nextflow": "25.04.6"
},
"timestamp": "2024-11-28T14:08:54.36318984"
"timestamp": "2025-10-28T13:22:38.810477312"
},
"homo_sapiens-test_rnaseq-stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
],
"log": [
[
{
"id": "test",
"single_end": false
},
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"transcript_fasta": [
"versions_trinity": [
[
{
"id": "test",
"single_end": false
},
"test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
"TRINITY",
"trinity",
"2.15.2"
]
],
"versions": [
"versions.yml:md5,1c631aefa156e739b773679c471467c1"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
"nextflow": "25.04.6"
},
"timestamp": "2024-11-28T14:09:00.571900709"
"timestamp": "2025-10-28T13:49:50.612026008"
}
}
}