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fellen31mashehu
fellen31
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mashehu
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Bump TRGT to 4.1.0 (#9514)
* Bump TRGT to 4.1.0 * Switch to topics * Update modules/nf-core/trgt/genotype/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
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15 files changed

+219
-93
lines changed

15 files changed

+219
-93
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‎modules/nf-core/trgt/genotype/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
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- conda-forge
55
- bioconda
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dependencies:
7-
- bioconda::trgt=4.0.0
7+
- bioconda::trgt=4.1.0

‎modules/nf-core/trgt/genotype/main.nf‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process TRGT_GENOTYPE {
44

55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/trgt:4.0.0--h9ee0642_0':
8-
'biocontainers/trgt:4.0.0--h9ee0642_0' }"
7+
'https://depot.galaxyproject.org/singularity/trgt:4.1.0--h9ee0642_0':
8+
'biocontainers/trgt:4.1.0--h9ee0642_0' }"
99

1010
input:
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tuple val(meta) , path(bam), path(bai), val(karyotype)
@@ -15,8 +15,8 @@ process TRGT_GENOTYPE {
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1616
output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
18-
tuple val(meta), path("*.spanning.bam"), emit: bam , optional: true
19-
path "versions.yml" , emit: versions
18+
tuple val(meta), path("*.spanning.bam"), emit: bam, optional: true
19+
tuple val("${task.process}"), val('trgt'), eval("trgt --version | sed 's/.* //g'"), emit: versions_trgt, topic: versions
2020

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when:
2222
task.ext.when == null || task.ext.when

‎modules/nf-core/trgt/genotype/meta.yml‎

Lines changed: 21 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -94,14 +94,28 @@ output:
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description: BAM file with pieces of reads aligning to repeats
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pattern: "*.spanning.bam"
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ontologies: []
97-
versions:
98-
- versions.yml:
99-
type: file
100-
description: File containing software versions
101-
pattern: "versions.yml"
97+
versions_trgt:
98+
- - ${task.process}:
99+
type: string
100+
description: The name of the process
101+
- trgt:
102+
type: string
103+
description: The name of the tool
104+
- trgt --version | sed 's/.* //g':
105+
type: eval
106+
description: The expression to obtain the version of the tool
102107

103-
ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
108+
topics:
109+
versions:
110+
- - ${task.process}:
111+
type: string
112+
description: The name of the process
113+
- trgt:
114+
type: string
115+
description: The name of the tool
116+
- trgt --version | sed 's/.* //g':
117+
type: eval
118+
description: The expression to obtain the version
105119
authors:
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- "@Schmytzi"
107121
- "@fellen31"

‎modules/nf-core/trgt/genotype/tests/main.nf.test‎

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Original file line numberDiff line numberDiff line change
@@ -59,7 +59,9 @@ nextflow_process {
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then {
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assertAll(
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{ assert process.success },
62-
{ assert snapshot(process.out).match() }
62+
{ assert snapshot(
63+
process.out,
64+
).match() }
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)
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}
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‎modules/nf-core/trgt/genotype/tests/main.nf.test.snap‎

Lines changed: 60 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -7,46 +7,54 @@
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{
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"id": "test"
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},
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"test.vcf.gz:md5,9d5f7877193d0c8a6fbce7c9f82ab05b"
10+
"test.vcf.gz:md5,cb694061956ddcd63772baf9a0720624"
1111
]
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],
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"1": [
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[
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{
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"id": "test"
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},
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"test.spanning.bam:md5,22cb334e5936fa940c3a78c89ba7477c"
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"test.spanning.bam:md5,47da98a17e3bc7b4b234c59a435a38ca"
1919
]
2020
],
2121
"2": [
22-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
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[
23+
"TRGT_GENOTYPE",
24+
"trgt",
25+
"4.1.0-39fa24c"
26+
]
2327
],
2428
"bam": [
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[
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{
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"id": "test"
2832
},
29-
"test.spanning.bam:md5,22cb334e5936fa940c3a78c89ba7477c"
33+
"test.spanning.bam:md5,47da98a17e3bc7b4b234c59a435a38ca"
3034
]
3135
],
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"vcf": [
3337
[
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{
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"id": "test"
3640
},
37-
"test.vcf.gz:md5,9d5f7877193d0c8a6fbce7c9f82ab05b"
41+
"test.vcf.gz:md5,cb694061956ddcd63772baf9a0720624"
3842
]
3943
],
40-
"versions": [
41-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
44+
"versions_trgt": [
45+
[
46+
"TRGT_GENOTYPE",
47+
"trgt",
48+
"4.1.0-39fa24c"
49+
]
4250
]
4351
}
4452
],
4553
"meta": {
4654
"nf-test": "0.9.2",
4755
"nextflow": "25.04.6"
4856
},
49-
"timestamp": "2025-10-23T11:19:06.149363798"
57+
"timestamp": "2025-12-09T16:16:00.489435938"
5058
},
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"homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": {
5260
"content": [
@@ -56,46 +64,54 @@
5664
{
5765
"id": "test"
5866
},
59-
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
67+
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
6068
]
6169
],
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"1": [
6371
[
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{
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"id": "test"
6674
},
67-
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
75+
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
6876
]
6977
],
7078
"2": [
71-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
79+
[
80+
"TRGT_GENOTYPE",
81+
"trgt",
82+
"4.1.0-39fa24c"
83+
]
7284
],
7385
"bam": [
7486
[
7587
{
7688
"id": "test"
7789
},
78-
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
90+
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
7991
]
8092
],
8193
"vcf": [
8294
[
8395
{
8496
"id": "test"
8597
},
86-
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
98+
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
8799
]
88100
],
89-
"versions": [
90-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
101+
"versions_trgt": [
102+
[
103+
"TRGT_GENOTYPE",
104+
"trgt",
105+
"4.1.0-39fa24c"
106+
]
91107
]
92108
}
93109
],
94110
"meta": {
95111
"nf-test": "0.9.2",
96112
"nextflow": "25.04.6"
97113
},
98-
"timestamp": "2025-10-23T11:19:21.404862883"
114+
"timestamp": "2025-12-09T16:16:15.759484541"
99115
},
100116
"homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": {
101117
"content": [
@@ -117,7 +133,11 @@
117133
]
118134
],
119135
"2": [
120-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
136+
[
137+
"TRGT_GENOTYPE",
138+
"trgt",
139+
"4.1.0-39fa24c"
140+
]
121141
],
122142
"bam": [
123143
[
@@ -135,16 +155,20 @@
135155
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
136156
]
137157
],
138-
"versions": [
139-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
158+
"versions_trgt": [
159+
[
160+
"TRGT_GENOTYPE",
161+
"trgt",
162+
"4.1.0-39fa24c"
163+
]
140164
]
141165
}
142166
],
143167
"meta": {
144168
"nf-test": "0.9.2",
145169
"nextflow": "25.04.6"
146170
},
147-
"timestamp": "2025-10-23T11:19:16.057879354"
171+
"timestamp": "2025-12-09T16:16:10.709433028"
148172
},
149173
"homo sapiens - [bam,bai,[]], [fa,fai], bed": {
150174
"content": [
@@ -154,45 +178,53 @@
154178
{
155179
"id": "test"
156180
},
157-
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
181+
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
158182
]
159183
],
160184
"1": [
161185
[
162186
{
163187
"id": "test"
164188
},
165-
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
189+
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
166190
]
167191
],
168192
"2": [
169-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
193+
[
194+
"TRGT_GENOTYPE",
195+
"trgt",
196+
"4.1.0-39fa24c"
197+
]
170198
],
171199
"bam": [
172200
[
173201
{
174202
"id": "test"
175203
},
176-
"test.spanning.bam:md5,0f1755fd47e7c942fda2282c5da2e8e8"
204+
"test.spanning.bam:md5,1370db3a5d025cdde50676fab4235c5f"
177205
]
178206
],
179207
"vcf": [
180208
[
181209
{
182210
"id": "test"
183211
},
184-
"test.vcf.gz:md5,03899fb4a8ca115e54a1db46800096cb"
212+
"test.vcf.gz:md5,2015f1ef3d10bf8ce99882099b61b185"
185213
]
186214
],
187-
"versions": [
188-
"versions.yml:md5,cf70c46a111ed5f7a9bdd432b6f579b6"
215+
"versions_trgt": [
216+
[
217+
"TRGT_GENOTYPE",
218+
"trgt",
219+
"4.1.0-39fa24c"
220+
]
189221
]
190222
}
191223
],
192224
"meta": {
193225
"nf-test": "0.9.2",
194226
"nextflow": "25.04.6"
195227
},
196-
"timestamp": "2025-10-23T11:19:10.595588655"
228+
"timestamp": "2025-12-09T16:16:05.648952742"
197229
}
198230
}

‎modules/nf-core/trgt/merge/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::trgt=4.0.0
7+
- bioconda::trgt=4.1.0

‎modules/nf-core/trgt/merge/main.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process TRGT_MERGE {
44

55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/trgt:4.0.0--h9ee0642_0':
8-
'biocontainers/trgt:4.0.0--h9ee0642_0' }"
7+
'https://depot.galaxyproject.org/singularity/trgt:4.1.0--h9ee0642_0':
8+
'biocontainers/trgt:4.1.0--h9ee0642_0' }"
99

1010
input:
1111
tuple val(meta) , path(vcfs), path(tbis)
@@ -14,7 +14,7 @@ process TRGT_MERGE {
1414

1515
output:
1616
tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
17-
path "versions.yml" , emit: versions
17+
tuple val("${task.process}"), val('trgt'), eval("trgt --version | sed 's/.* //g'"), emit: versions_trgt, topic: versions
1818

1919
when:
2020
task.ext.when == null || task.ext.when

‎modules/nf-core/trgt/merge/meta.yml‎

Lines changed: 21 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -72,14 +72,28 @@ output:
7272
description: "Merged output file"
7373
pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
7474
ontologies: []
75-
versions:
76-
- versions.yml:
77-
type: file
78-
description: File containing software versions
79-
pattern: "versions.yml"
75+
versions_trgt:
76+
- - ${task.process}:
77+
type: string
78+
description: The name of the process
79+
- trgt:
80+
type: string
81+
description: The name of the tool
82+
- trgt --version | sed 's/.* //g':
83+
type: eval
84+
description: The expression to obtain the version of the tool
8085

81-
ontologies:
82-
- edam: http://edamontology.org/format_3750 # YAML
86+
topics:
87+
versions:
88+
- - ${task.process}:
89+
type: string
90+
description: The name of the process
91+
- trgt:
92+
type: string
93+
description: The name of the tool
94+
- trgt --version | sed 's/.* //g':
95+
type: eval
96+
description: The expression to obtain the version
8397
authors:
8498
- "@Schmytzi"
8599
maintainers:

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