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Blobtk depth versions topic (#10280)
* Version topics for blobtk depth * Version topics for blobtk plot
1 parent d753d08 commit f0ee159

7 files changed

Lines changed: 98 additions & 50 deletions

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‎modules/nf-core/blobtk/depth/main.nf‎

Lines changed: 1 addition & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ process BLOBTK_DEPTH {
1212

1313
output:
1414
tuple val(meta), path('*.regions.bed.gz') , emit: bed
15-
path "versions.yml" , emit: versions
15+
tuple val("${task.process}"), val("blobtk"), eval("blobtk --version | cut -d' ' -f2"), topic: versions, emit: versions_blobtk
1616

1717
when:
1818
task.ext.when == null || task.ext.when
@@ -25,11 +25,6 @@ process BLOBTK_DEPTH {
2525
-b ${bam} \\
2626
$args \\
2727
-O ${prefix}.regions.bed.gz \\
28-
29-
cat <<-END_VERSIONS > versions.yml
30-
"${task.process}":
31-
blobtk: \$(blobtk --version | cut -d' ' -f2)
32-
END_VERSIONS
3328
"""
3429

3530
stub:

‎modules/nf-core/blobtk/depth/meta.yml‎

Lines changed: 20 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -50,13 +50,27 @@ output:
5050
type: file
5151
description: |
5252
Bed file describing the depth of regions across the genome.
53+
versions_blobtk:
54+
- - ${task.process}:
55+
type: string
56+
description: The name of the process
57+
- blobtk:
58+
type: string
59+
description: The name of the tool
60+
- "blobtk --version | cut -d' ' -f2":
61+
type: eval
62+
description: The expression to obtain the version of the tool
63+
topics:
5364
versions:
54-
- versions.yml:
55-
type: file
56-
description: File containing software versions
57-
pattern: "versions.yml"
58-
ontologies:
59-
- edam: http://edamontology.org/format_3750 # YAML
65+
- - ${task.process}:
66+
type: string
67+
description: The name of the process
68+
- blobtk:
69+
type: string
70+
description: The name of the tool
71+
- "blobtk --version | cut -d' ' -f2":
72+
type: eval
73+
description: The expression to obtain the version of the tool
6074
authors:
6175
- "@DLBPointon"
6276
maintainers:

‎modules/nf-core/blobtk/depth/tests/main.nf.test.snap‎

Lines changed: 29 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,11 @@
1111
]
1212
],
1313
"1": [
14-
"versions.yml:md5,e6ef8abfede721f3dacd8a8e77e19c61"
14+
[
15+
"BLOBTK_DEPTH",
16+
"blobtk",
17+
"0.7.1"
18+
]
1519
],
1620
"bed": [
1721
[
@@ -21,16 +25,20 @@
2125
"test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
2226
]
2327
],
24-
"versions": [
25-
"versions.yml:md5,e6ef8abfede721f3dacd8a8e77e19c61"
28+
"versions_blobtk": [
29+
[
30+
"BLOBTK_DEPTH",
31+
"blobtk",
32+
"0.7.1"
33+
]
2634
]
2735
}
2836
],
2937
"meta": {
30-
"nf-test": "0.9.2",
31-
"nextflow": "25.04.6"
38+
"nf-test": "0.9.3",
39+
"nextflow": "25.10.0"
3240
},
33-
"timestamp": "2025-09-05T11:10:43.310311149"
41+
"timestamp": "2026-02-27T11:03:02.967972666"
3442
},
3543
"bacteroides fragilis - bam and bai": {
3644
"content": [
@@ -44,7 +52,11 @@
4452
]
4553
],
4654
"1": [
47-
"versions.yml:md5,e6ef8abfede721f3dacd8a8e77e19c61"
55+
[
56+
"BLOBTK_DEPTH",
57+
"blobtk",
58+
"0.7.1"
59+
]
4860
],
4961
"bed": [
5062
[
@@ -54,15 +66,19 @@
5466
"test.regions.bed.gz:md5,2519fb9821b18e916637052efdbb59ad"
5567
]
5668
],
57-
"versions": [
58-
"versions.yml:md5,e6ef8abfede721f3dacd8a8e77e19c61"
69+
"versions_blobtk": [
70+
[
71+
"BLOBTK_DEPTH",
72+
"blobtk",
73+
"0.7.1"
74+
]
5975
]
6076
}
6177
],
6278
"meta": {
63-
"nf-test": "0.9.2",
64-
"nextflow": "25.04.6"
79+
"nf-test": "0.9.3",
80+
"nextflow": "25.10.0"
6581
},
66-
"timestamp": "2025-09-05T11:10:34.092889632"
82+
"timestamp": "2026-02-27T11:02:56.318306565"
6783
}
68-
}
84+
}

‎modules/nf-core/blobtk/plot/main.nf‎

Lines changed: 1 addition & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ process BLOBTK_PLOT {
2424

2525
output:
2626
tuple val(meta), path("*.png"), emit: png
27-
path "versions.yml" , emit: versions
27+
tuple val("${task.process}"), val("blobtk"), eval("blobtk --version | cut -d' ' -f2"), topic: versions, emit: versions_blobtk
2828

2929
when:
3030
task.ext.when == null || task.ext.when
@@ -44,11 +44,6 @@ process BLOBTK_PLOT {
4444
-d $resource \\
4545
$args \\
4646
-o ${prefix}.png
47-
48-
cat <<-END_VERSIONS > versions.yml
49-
"${task.process}":
50-
blobtk: \$(blobtk --version | cut -d' ' -f2)
51-
END_VERSIONS
5247
"""
5348

5449
stub:

‎modules/nf-core/blobtk/plot/meta.yml‎

Lines changed: 20 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -60,13 +60,27 @@ output:
6060
Blobplot PNG results of input arguments.
6161
ontologies:
6262
- edam: http://edamontology.org/format_3603
63+
versions_blobtk:
64+
- - ${task.process}:
65+
type: string
66+
description: The name of the process
67+
- blobtk:
68+
type: string
69+
description: The name of the tool
70+
- "blobtk --version | cut -d' ' -f2":
71+
type: eval
72+
description: The expression to obtain the version of the tool
73+
topics:
6374
versions:
64-
- versions.yml:
65-
type: file
66-
description: File containing software versions
67-
pattern: "versions.yml"
68-
ontologies:
69-
- edam: http://edamontology.org/format_3750 # YAML
75+
- - ${task.process}:
76+
type: string
77+
description: The name of the process
78+
- blobtk:
79+
type: string
80+
description: The name of the tool
81+
- "blobtk --version | cut -d' ' -f2":
82+
type: eval
83+
description: The expression to obtain the version of the tool
7084
authors:
7185
- "@DLBPointon"
7286
maintainers:

‎modules/nf-core/blobtk/plot/tests/main.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ nextflow_process {
4242
{
4343
assert snapshot(
4444
process.out.png.collect { meta, image -> [meta, file(image).name] },
45-
process.out.versions
45+
process.out.findAll { key, val -> key.startsWith("versions") }
4646
).match()
4747
}
4848
)

‎modules/nf-core/blobtk/plot/tests/main.nf.test.snap‎

Lines changed: 26 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -9,15 +9,21 @@
99
"test_BLOB_VIEW.png"
1010
]
1111
],
12-
[
13-
"versions.yml:md5,9855c180bfc28c1fd411132466496d76"
14-
]
12+
{
13+
"versions_blobtk": [
14+
[
15+
"BLOBTK_PLOT",
16+
"blobtk",
17+
"0.7.1"
18+
]
19+
]
20+
}
1521
],
1622
"meta": {
17-
"nf-test": "0.9.2",
18-
"nextflow": "25.04.6"
23+
"nf-test": "0.9.3",
24+
"nextflow": "25.10.0"
1925
},
20-
"timestamp": "2025-09-10T10:49:45.919675817"
26+
"timestamp": "2026-02-27T11:07:25.205080395"
2127
},
2228
"bacteroides fragilis - fasta - stub": {
2329
"content": [
@@ -31,7 +37,11 @@
3137
]
3238
],
3339
"1": [
34-
"versions.yml:md5,9855c180bfc28c1fd411132466496d76"
40+
[
41+
"BLOBTK_PLOT",
42+
"blobtk",
43+
"0.7.1"
44+
]
3545
],
3646
"png": [
3747
[
@@ -41,15 +51,19 @@
4151
"test_BLOB_VIEW.png:md5,d41d8cd98f00b204e9800998ecf8427e"
4252
]
4353
],
44-
"versions": [
45-
"versions.yml:md5,9855c180bfc28c1fd411132466496d76"
54+
"versions_blobtk": [
55+
[
56+
"BLOBTK_PLOT",
57+
"blobtk",
58+
"0.7.1"
59+
]
4660
]
4761
}
4862
],
4963
"meta": {
50-
"nf-test": "0.9.2",
51-
"nextflow": "25.04.6"
64+
"nf-test": "0.9.3",
65+
"nextflow": "25.10.0"
5266
},
53-
"timestamp": "2025-09-10T10:49:53.414843461"
67+
"timestamp": "2026-02-27T11:03:48.618241783"
5468
}
5569
}

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