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Merged
mashehu merged 5 commits into from
Dec 9, 2025
+219 −93
Merged

Bump TRGT to 4.1.0 #9514

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d10682e
Bump TRGT to 4.1.0
fellen31 Dec 6, 2025
4f0e9c8
Switch to topics
fellen31 Dec 6, 2025
d974117
Update modules/nf-core/trgt/genotype/tests/main.nf.test
fellen31 Dec 9, 2025
0a3e2d8
remove duplicate versions
fellen31 Dec 9, 2025
784b15b
Merge branch 'master' into bump-trgt
fellen31 Dec 9, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/trgt/genotype/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::trgt=4.0.0
- bioconda::trgt=4.1.0
8 changes: 4 additions & 4 deletions modules/nf-core/trgt/genotype/main.nf
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Expand Up @@ -4,8 +4,8 @@ process TRGT_GENOTYPE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/trgt:4.0.0--h9ee0642_0':
'biocontainers/trgt:4.0.0--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/trgt:4.1.0--h9ee0642_0':
'biocontainers/trgt:4.1.0--h9ee0642_0' }"

input:
tuple val(meta) , path(bam), path(bai), val(karyotype)
Expand All @@ -15,8 +15,8 @@ process TRGT_GENOTYPE {

output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.spanning.bam"), emit: bam , optional: true
path "versions.yml" , emit: versions
tuple val(meta), path("*.spanning.bam"), emit: bam, optional: true
tuple val("${task.process}"), val('trgt'), eval("trgt --version | sed 's/.* //g'"), emit: versions_trgt, topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down
28 changes: 21 additions & 7 deletions modules/nf-core/trgt/genotype/meta.yml
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Expand Up @@ -94,14 +94,28 @@ output:
description: BAM file with pieces of reads aligning to repeats
pattern: "*.spanning.bam"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
versions_trgt:
- - ${task.process}:
type: string
description: The name of the process
- trgt:
type: string
description: The name of the tool
- trgt --version | sed 's/.* //g':
type: eval
description: The expression to obtain the version of the tool

ontologies:
- edam: http://edamontology.org/format_3750 # YAML
topics:
versions:
- - ${task.process}:
type: string
description: The name of the process
- trgt:
type: string
description: The name of the tool
- trgt --version | sed 's/.* //g':
type: eval
description: The expression to obtain the version
authors:
- "@Schmytzi"
- "@fellen31"
Expand Down
4 changes: 3 additions & 1 deletion modules/nf-core/trgt/genotype/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out,
).match() }
)
}

Expand Down
88 changes: 60 additions & 28 deletions modules/nf-core/trgt/genotype/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,46 +7,54 @@
{
"id": "test"
},
"test.vcf.gz:md5,9d5f7877193d0c8a6fbce7c9f82ab05b"
"test.vcf.gz:md5,cb694061956ddcd63772baf9a0720624"
]
],
"1": [
[
{
"id": "test"
},
"test.spanning.bam:md5,22cb334e5936fa940c3a78c89ba7477c"
"test.spanning.bam:md5,47da98a17e3bc7b4b234c59a435a38ca"
]
],
"2": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
],
"bam": [
[
{
"id": "test"
},
"test.spanning.bam:md5,22cb334e5936fa940c3a78c89ba7477c"
"test.spanning.bam:md5,47da98a17e3bc7b4b234c59a435a38ca"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,9d5f7877193d0c8a6fbce7c9f82ab05b"
"test.vcf.gz:md5,cb694061956ddcd63772baf9a0720624"
]
],
"versions": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
"versions_trgt": [
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-10-23T11:19:06.149363798"
"timestamp": "2025-12-09T16:16:00.489435938"
},
"homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": {
"content": [
Expand All @@ -56,46 +64,54 @@
{
"id": "test"
},
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
]
],
"1": [
[
{
"id": "test"
},
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
]
],
"2": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
],
"bam": [
[
{
"id": "test"
},
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
]
],
"versions": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
"versions_trgt": [
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-10-23T11:19:21.404862883"
"timestamp": "2025-12-09T16:16:15.759484541"
},
"homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": {
"content": [
Expand All @@ -117,7 +133,11 @@
]
],
"2": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
],
"bam": [
[
Expand All @@ -135,16 +155,20 @@
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
"versions_trgt": [
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-10-23T11:19:16.057879354"
"timestamp": "2025-12-09T16:16:10.709433028"
},
"homo sapiens - [bam,bai,[]], [fa,fai], bed": {
"content": [
Expand All @@ -154,45 +178,53 @@
{
"id": "test"
},
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
]
],
"1": [
[
{
"id": "test"
},
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
]
],
"2": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
],
"bam": [
[
{
"id": "test"
},
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
]
],
"versions": [
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
"versions_trgt": [
[
"TRGT_GENOTYPE",
"trgt",
"4.1.0-39fa24c"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-10-23T11:19:10.595588655"
"timestamp": "2025-12-09T16:16:05.648952742"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/trgt/merge/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::trgt=4.0.0
- bioconda::trgt=4.1.0
6 changes: 3 additions & 3 deletions modules/nf-core/trgt/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TRGT_MERGE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/trgt:4.0.0--h9ee0642_0':
'biocontainers/trgt:4.0.0--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/trgt:4.1.0--h9ee0642_0':
'biocontainers/trgt:4.1.0--h9ee0642_0' }"

input:
tuple val(meta) , path(vcfs), path(tbis)
Expand All @@ -14,7 +14,7 @@ process TRGT_MERGE {

output:
tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('trgt'), eval("trgt --version | sed 's/.* //g'"), emit: versions_trgt, topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down
28 changes: 21 additions & 7 deletions modules/nf-core/trgt/merge/meta.yml
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Expand Up @@ -72,14 +72,28 @@ output:
description: "Merged output file"
pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
versions_trgt:
- - ${task.process}:
type: string
description: The name of the process
- trgt:
type: string
description: The name of the tool
- trgt --version | sed 's/.* //g':
type: eval
description: The expression to obtain the version of the tool

ontologies:
- edam: http://edamontology.org/format_3750 # YAML
topics:
versions:
- - ${task.process}:
type: string
description: The name of the process
- trgt:
type: string
description: The name of the tool
- trgt --version | sed 's/.* //g':
type: eval
description: The expression to obtain the version
authors:
- "@Schmytzi"
maintainers:
Expand Down
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