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LouisLeNezetLouisLeNezet
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Update to topics deepbgc/* (nf-core#11275)
* Update to topics * Update meta
1 parent 5e1bb13 commit 6c4ed3a

8 files changed

Lines changed: 208 additions & 548 deletions

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‎modules/nf-core/deepbgc/download/main.nf‎

Lines changed: 8 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ process DEEPBGC_DOWNLOAD {
88

99
output:
1010
path "deepbgc_db/", emit: db
11-
path "versions.yml", emit: versions
11+
tuple val("${task.process}"), val('deepbgc'), eval("deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'"), emit: versions_deepbgc, topic: versions
1212

1313
when:
1414
task.ext.when == null || task.ext.when
@@ -20,20 +20,17 @@ process DEEPBGC_DOWNLOAD {
2020
2121
deepbgc \\
2222
download
23-
24-
cat <<-END_VERSIONS > versions.yml
25-
"${task.process}":
26-
deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
27-
END_VERSIONS
2823
"""
2924

3025
stub:
3126
"""
32-
mkdir -p deepbgc_db
27+
mkdir -p deepbgc_db/0.1.0/classifier deepbgc_db/0.1.0/detector deepbgc_db/common
28+
29+
touch deepbgc_db/common/Pfam-A.31.0.clans.tsv
30+
touch deepbgc_db/common/Pfam-A.31.0.hmm.{,h3f,h3i,h3m,h3p}
3331
34-
cat <<-END_VERSIONS > versions.yml
35-
"${task.process}":
36-
deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
37-
END_VERSIONS
32+
touch deepbgc_db/0.1.0/classifier/product_{activity,class}.pkl
33+
touch deepbgc_db/0.1.0/detector/clusterfinder_{geneborder,original,retrained}.pkl
34+
touch deepbgc_db/0.1.0/detector/deepbgc.pkl
3835
"""
3936
}

‎modules/nf-core/deepbgc/download/meta.yml‎

Lines changed: 20 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -27,13 +27,27 @@ output:
2727
type: directory
2828
description: Directory containing the DeepBGC database
2929
pattern: "deepbgc_db/"
30+
versions_deepbgc:
31+
- - ${task.process}:
32+
type: string
33+
description: The name of the process
34+
- deepbgc:
35+
type: string
36+
description: The name of the tool
37+
- deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//':
38+
type: eval
39+
description: The expression to obtain the version of the tool
40+
topics:
3041
versions:
31-
- versions.yml:
32-
type: file
33-
description: File containing software versions
34-
pattern: "versions.yml"
35-
ontologies:
36-
- edam: http://edamontology.org/format_3750 # YAML
42+
- - ${task.process}:
43+
type: string
44+
description: The name of the process
45+
- deepbgc:
46+
type: string
47+
description: The name of the tool
48+
- deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//':
49+
type: eval
50+
description: The expression to obtain the version of the tool
3751
authors:
3852
- "@louperelo"
3953
maintainers:

‎modules/nf-core/deepbgc/download/tests/main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ nextflow_process {
2121
then {
2222
assertAll(
2323
{ assert process.success },
24-
{ assert snapshot(process.out).match() }
24+
{ assert snapshot(sanitizeOutput(process.out)).match() }
2525
)
2626
}
2727
}
@@ -40,7 +40,7 @@ nextflow_process {
4040
then {
4141
assertAll(
4242
{ assert process.success },
43-
{ assert snapshot(process.out).match() }
43+
{ assert snapshot(sanitizeOutput(process.out)).match() }
4444
)
4545
}
4646
}

‎modules/nf-core/deepbgc/download/tests/main.nf.test.snap‎

Lines changed: 38 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -2,34 +2,49 @@
22
"deepbgc download db - stub": {
33
"content": [
44
{
5-
"0": [
5+
"db": [
66
[
7-
7+
[
8+
[
9+
"product_activity.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
10+
"product_class.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
11+
],
12+
[
13+
"clusterfinder_geneborder.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
14+
"clusterfinder_original.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
15+
"clusterfinder_retrained.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
16+
"deepbgc.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
17+
]
18+
],
19+
[
20+
"Pfam-A.31.0.clans.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
21+
"Pfam-A.31.0.hmm.:md5,d41d8cd98f00b204e9800998ecf8427e",
22+
"Pfam-A.31.0.hmm.h3f:md5,d41d8cd98f00b204e9800998ecf8427e",
23+
"Pfam-A.31.0.hmm.h3i:md5,d41d8cd98f00b204e9800998ecf8427e",
24+
"Pfam-A.31.0.hmm.h3m:md5,d41d8cd98f00b204e9800998ecf8427e",
25+
"Pfam-A.31.0.hmm.h3p:md5,d41d8cd98f00b204e9800998ecf8427e"
26+
]
827
]
928
],
10-
"1": [
11-
"versions.yml:md5,4130f2ce0a4d43fc3d8e04f4935f908b"
12-
],
13-
"db": [
29+
"versions_deepbgc": [
1430
[
15-
31+
"DEEPBGC_DOWNLOAD",
32+
"deepbgc",
33+
"0.1.31"
1634
]
17-
],
18-
"versions": [
19-
"versions.yml:md5,4130f2ce0a4d43fc3d8e04f4935f908b"
2035
]
2136
}
2237
],
38+
"timestamp": "2026-04-23T12:43:58.416881649",
2339
"meta": {
24-
"nf-test": "0.9.2",
25-
"nextflow": "24.10.2"
26-
},
27-
"timestamp": "2024-12-16T13:16:09.517281467"
40+
"nf-test": "0.9.5",
41+
"nextflow": "26.03.2"
42+
}
2843
},
2944
"deepbgc download db": {
3045
"content": [
3146
{
32-
"0": [
47+
"db": [
3348
[
3449
[
3550
[
@@ -53,42 +68,19 @@
5368
]
5469
]
5570
],
56-
"1": [
57-
"versions.yml:md5,4130f2ce0a4d43fc3d8e04f4935f908b"
58-
],
59-
"db": [
71+
"versions_deepbgc": [
6072
[
61-
[
62-
[
63-
"product_activity.pkl:md5,90f0c010460e9df882cb057664a49f30",
64-
"product_class.pkl:md5,f78a2eda240403d2f40643d42202f3ac"
65-
],
66-
[
67-
"clusterfinder_geneborder.pkl:md5,ca4be7031ae9f70780f17c616a4fa5b5",
68-
"clusterfinder_original.pkl:md5,2ca2429bb9bc99a401d1093c376b37aa",
69-
"clusterfinder_retrained.pkl:md5,65679a3b61c562ff4b84bdb574bb6d93",
70-
"deepbgc.pkl:md5,7e9218be79ba45bc9adb23bed3845dc1"
71-
]
72-
],
73-
[
74-
"Pfam-A.31.0.clans.tsv:md5,a0a4590ffb2b33b83ef2b28f6ead886b",
75-
"Pfam-A.31.0.hmm:md5,79a3328e4c95b13949a4489b19959fc5",
76-
"Pfam-A.31.0.hmm.h3f:md5,cbca323cf8dd4e5e7c109114ec444162",
77-
"Pfam-A.31.0.hmm.h3i:md5,5242332a3f6a60cd1ab634cd9331afd6",
78-
"Pfam-A.31.0.hmm.h3m:md5,1fe946fa2b3bcde1d4b2bad732bce612",
79-
"Pfam-A.31.0.hmm.h3p:md5,27b98a1ded123b6a1ef72db01927017c"
80-
]
73+
"DEEPBGC_DOWNLOAD",
74+
"deepbgc",
75+
"0.1.31"
8176
]
82-
],
83-
"versions": [
84-
"versions.yml:md5,4130f2ce0a4d43fc3d8e04f4935f908b"
8577
]
8678
}
8779
],
80+
"timestamp": "2026-04-23T12:18:55.049649444",
8881
"meta": {
89-
"nf-test": "0.9.2",
90-
"nextflow": "24.10.2"
91-
},
92-
"timestamp": "2024-12-16T13:15:16.323023111"
82+
"nf-test": "0.9.5",
83+
"nextflow": "26.03.2"
84+
}
9385
}
9486
}

‎modules/nf-core/deepbgc/pipeline/main.nf‎

Lines changed: 2 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,8 @@ process DEEPBGC_PIPELINE {
2323
tuple val(meta), path("${prefix}/evaluation/${prefix}.pr.png"), optional: true, emit: pr_png
2424
tuple val(meta), path("${prefix}/evaluation/${prefix}.roc.png"), optional: true, emit: roc_png
2525
tuple val(meta), path("${prefix}/evaluation/${prefix}.score.png"), optional: true, emit: score_png
26-
path "versions.yml", emit: versions
26+
tuple val("${task.process}"), val('deepbgc'), eval("deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//'"), emit: versions_deepbgc, topic: versions
27+
tuple val("${task.process}"), val('prodigal'), eval("prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//'"), emit: versions_prodigal, topic: versions
2728

2829
when:
2930
task.ext.when == null || task.ext.when
@@ -46,12 +47,6 @@ process DEEPBGC_PIPELINE {
4647
for i in \$(find -name '${genome.baseName}*' -type f); do
4748
mv \$i \${i/${genome.baseName}/${prefix}};
4849
done
49-
50-
cat <<-END_VERSIONS > versions.yml
51-
"${task.process}":
52-
deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
53-
prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
54-
END_VERSIONS
5550
"""
5651

5752
stub:
@@ -69,11 +64,5 @@ process DEEPBGC_PIPELINE {
6964
touch ${prefix}/evaluation/${prefix}.pr.png
7065
touch ${prefix}/evaluation/${prefix}.roc.png
7166
touch ${prefix}/evaluation/${prefix}.score.png
72-
73-
cat <<-END_VERSIONS > versions.yml
74-
"${task.process}":
75-
deepbgc: \$(echo \$(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
76-
prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
77-
END_VERSIONS
7867
"""
7968
}

‎modules/nf-core/deepbgc/pipeline/meta.yml‎

Lines changed: 39 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -158,13 +158,46 @@ output:
158158
description: BGC detection scores of each Pfam domain in genomic order
159159
pattern: "*.{score.png}"
160160
ontologies: []
161+
versions_deepbgc:
162+
- - ${task.process}:
163+
type: string
164+
description: The name of the process
165+
- deepbgc:
166+
type: string
167+
description: The name of the tool
168+
- deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//':
169+
type: eval
170+
description: The expression to obtain the version of the tool
171+
versions_prodigal:
172+
- - ${task.process}:
173+
type: string
174+
description: The name of the process
175+
- prodigal:
176+
type: string
177+
description: The name of the tool
178+
- prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//':
179+
type: eval
180+
description: The expression to obtain the version of the tool
181+
topics:
161182
versions:
162-
- versions.yml:
163-
type: file
164-
description: File containing software versions
165-
pattern: "versions.yml"
166-
ontologies:
167-
- edam: http://edamontology.org/format_3750 # YAML
183+
- - ${task.process}:
184+
type: string
185+
description: The name of the process
186+
- deepbgc:
187+
type: string
188+
description: The name of the tool
189+
- deepbgc info 2>&1 | sed '6!d;s/.*= version //;s/ .*//':
190+
type: eval
191+
description: The expression to obtain the version of the tool
192+
- - ${task.process}:
193+
type: string
194+
description: The name of the process
195+
- prodigal:
196+
type: string
197+
description: The name of the tool
198+
- prodigal -v 2>&1 | sed '2!d;s/Prodigal V//;s/:.*//':
199+
type: eval
200+
description: The expression to obtain the version of the tool
168201
authors:
169202
- "@louperelo"
170203
- "@jfy133"

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