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LouisLeNezetLouisLeNezet
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Update to topics braker3 (#11186)
Update to topics
1 parent 2fc6aef commit 08aea2f

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Lines changed: 227 additions & 133 deletions

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‎modules/nf-core/braker3/main.nf‎

Lines changed: 4 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,10 @@ process BRAKER3 {
2323
tuple val(meta), path("$prefix/hintsfile.gff") , emit: hintsfile , optional: true
2424
tuple val(meta), path("$prefix/braker.gff3") , emit: gff3 , optional: true
2525
tuple val(meta), path("$prefix/what-to-cite.txt") , emit: citations
26-
path "versions.yml" , emit: versions
26+
tuple val("${task.process}"), val('braker3'), eval("braker.pl --version 2>/dev/null | sed 's/braker.pl version //'"), emit: versions_braker3, topic: versions
27+
tuple val("${task.process}"), val('augustus'), eval("augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p'"), emit: versions_augustus, topic: versions
28+
tuple val("${task.process}"), val('genemark-etp'), eval("gmetp.pl |& sed -n 's/ETP version \\(.*\\)/\\1/p'"), emit: versions_genemarketp, topic: versions
29+
tuple val("${task.process}"), val('prothint'), eval("prothint.py --version |& sed 's/prothint.py //1'"), emit: versions_prothint, topic: versions
2730

2831
when:
2932
task.ext.when == null || task.ext.when
@@ -60,14 +63,6 @@ process BRAKER3 {
6063
$prot_arg \\
6164
$hints \\
6265
$args
63-
64-
cat <<-END_VERSIONS > versions.yml
65-
"${task.process}":
66-
braker3: \$(braker.pl --version 2>/dev/null | sed 's/braker.pl version //')
67-
augustus: \$(augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p')
68-
genemark-etp: \$(echo "\$(gmetp.pl || echo '')" | sed -n 's/ETP version \\(.*\\)/\\1/p')
69-
prothint: \$(prothint.py --version | sed 's/prothint.py //1')
70-
END_VERSIONS
7166
"""
7267

7368
stub:
@@ -87,13 +82,5 @@ process BRAKER3 {
8782
touch "$prefix/braker.log"
8883
touch "$prefix/what-to-cite.txt"
8984
$touch_gff
90-
91-
cat <<-END_VERSIONS > versions.yml
92-
"${task.process}":
93-
braker3: \$(braker.pl --version 2>/dev/null | sed 's/braker.pl version //')
94-
augustus: \$(augustus --version |& sed -n 's/AUGUSTUS (\\(.*\\)) is a gene .*/\\1/p')
95-
genemark-etp: \$(echo "\$(gmetp.pl || echo '')" | sed -n 's/ETP version \\(.*\\)/\\1/p')
96-
prothint: \$(prothint.py --version | sed 's/prothint.py //1')
97-
END_VERSIONS
9885
"""
9986
}

‎modules/nf-core/braker3/meta.yml‎

Lines changed: 146 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -15,9 +15,9 @@ tools:
1515
documentation: https://github.com/Gaius-Augustus/BRAKER
1616
tool_dev_url: https://github.com/Gaius-Augustus/BRAKER
1717
doi: "10.13140/RG.2.2.20047.36004"
18-
licence: ["Artistic-1.0"]
18+
licence:
19+
- "Artistic-1.0"
1920
identifier: biotools:braker3
20-
2121
input:
2222
- - meta:
2323
type: map
@@ -28,93 +28,187 @@ input:
2828
type: file
2929
description: Genome assembly fasta
3030
pattern: "*.{fasta,fa,fas,faa,fna}"
31-
- - bam:
32-
type: file
33-
description: BAM file of RNA-seq data to be passed to --bam
34-
pattern: "*.bam"
35-
- - rnaseq_sets_dirs:
36-
type: file
37-
description: Directories of RNA-seq data sets to be passed to --rnaseq_sets_dirs
38-
- - rnaseq_sets_ids:
39-
type: file
40-
description: IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids
41-
- - proteins:
42-
type: file
43-
description: Protein evidence to be passed to --proteins
44-
pattern: "*.{fasta,fa,fas,faa}"
45-
- - hintsfile:
46-
type: file
47-
description: Hintsfile to be passed to --hintsfile
48-
pattern: "*.{gff, gtf, gff3}"
31+
ontologies: []
32+
- bam:
33+
type: file
34+
description: BAM file of RNA-seq data to be passed to --bam
35+
pattern: "*.bam"
36+
ontologies: []
37+
- rnaseq_sets_dirs:
38+
type: file
39+
description: Directories of RNA-seq data sets to be passed to
40+
--rnaseq_sets_dirs
41+
ontologies: []
42+
- rnaseq_sets_ids:
43+
type: file
44+
description: IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids
45+
ontologies: []
46+
- proteins:
47+
type: file
48+
description: Protein evidence to be passed to --proteins
49+
pattern: "*.{fasta,fa,fas,faa}"
50+
ontologies: []
51+
- hintsfile:
52+
type: file
53+
description: Hintsfile to be passed to --hintsfile
54+
pattern: "*.{gff, gtf, gff3}"
55+
ontologies: []
4956
output:
5057
gtf:
5158
- - meta:
5259
type: file
5360
description: Gene transfer format file as output by BRAKER3
5461
pattern: "*.{gtf}"
55-
- $prefix/braker.gtf:
56-
type: file
57-
description: Gene transfer format file as output by BRAKER3
58-
pattern: "*.{gtf}"
62+
ontologies: []
63+
- $prefix/braker.gtf:
64+
type: file
65+
description: Gene transfer format file as output by BRAKER3
66+
pattern: "*.{gtf}"
67+
ontologies: []
5968
cds:
6069
- - meta:
70+
type: file
71+
description: Gene transfer format file as output by BRAKER3
72+
pattern: "*.{gtf}"
73+
ontologies: []
74+
- $prefix/braker.codingseq:
6175
type: file
6276
description: Coding sequence file as output by BRAKER3
6377
pattern: "*.{codingseq}"
64-
- $prefix/braker.codingseq:
65-
type: file
66-
description: Coding sequence file as output by BRAKER3
67-
pattern: "*.{codingseq}"
78+
ontologies: []
6879
aa:
6980
- - meta:
81+
type: file
82+
description: Gene transfer format file as output by BRAKER3
83+
pattern: "*.{gtf}"
84+
ontologies: []
85+
- $prefix/braker.aa:
7086
type: file
7187
description: Protein sequence file as output by BRAKER3
7288
pattern: "*.{aa}"
73-
- $prefix/braker.aa:
74-
type: file
75-
description: Protein sequence file as output by BRAKER3
76-
pattern: "*.{aa}"
89+
ontologies: []
7790
log:
7891
- - meta:
92+
type: file
93+
description: Gene transfer format file as output by BRAKER3
94+
pattern: "*.{gtf}"
95+
ontologies: []
96+
- $prefix/braker.log:
7997
type: file
8098
description: BRAKER3 log file
8199
pattern: "*.log"
82-
- $prefix/braker.log:
83-
type: file
84-
description: BRAKER3 log file
85-
pattern: "*.log"
100+
ontologies: []
86101
hintsfile:
87102
- - meta:
103+
type: file
104+
description: Gene transfer format file as output by BRAKER3
105+
pattern: "*.{gtf}"
106+
ontologies: []
107+
- $prefix/hintsfile.gff:
88108
type: file
89109
description: Hints file as output by BRAKER3
90110
pattern: "*hintsfile.{gff}"
91-
- $prefix/hintsfile.gff:
92-
type: file
93-
description: Hints file as output by BRAKER3
94-
pattern: "*hintsfile.{gff}"
111+
ontologies: []
95112
gff3:
96113
- - meta:
114+
type: file
115+
description: Gene transfer format file as output by BRAKER3
116+
pattern: "*.{gtf}"
117+
ontologies: []
118+
- $prefix/braker.gff3:
97119
type: file
98120
description: GFF3 file as output by BRAKER3
99121
pattern: "*.{gff3}"
100-
- $prefix/braker.gff3:
101-
type: file
102-
description: GFF3 file as output by BRAKER3
103-
pattern: "*.{gff3}"
122+
ontologies: []
104123
citations:
105124
- - meta:
125+
type: file
126+
description: Gene transfer format file as output by BRAKER3
127+
pattern: "*.{gtf}"
128+
ontologies: []
129+
- $prefix/what-to-cite.txt:
106130
type: file
107131
description: BRAKER3 citations
108132
pattern: "what-to-cite.txt"
109-
- "$prefix/what-to-cite.txt":
110-
type: file
111-
description: BRAKER3 citations
112-
pattern: "what-to-cite.txt"
133+
ontologies: []
134+
versions_braker3:
135+
- - ${task.process}:
136+
type: string
137+
description: The name of the process
138+
- braker3:
139+
type: string
140+
description: The name of the tool
141+
- braker.pl --version 2>/dev/null | sed 's/braker.pl version //':
142+
type: eval
143+
description: The expression to obtain the version of the tool
144+
versions_augustus:
145+
- - ${task.process}:
146+
type: string
147+
description: The name of the process
148+
- augustus:
149+
type: string
150+
description: The name of the tool
151+
- augustus --version |& sed -n 's/AUGUSTUS (\(.*\)) is a gene .*/\1/p':
152+
type: eval
153+
description: The expression to obtain the version of the tool
154+
versions_genemarketp:
155+
- - ${task.process}:
156+
type: string
157+
description: The name of the process
158+
- genemark-etp:
159+
type: string
160+
description: The name of the tool
161+
- gmetp.pl |& sed -n 's/ETP version \(.*\)/\1/p':
162+
type: eval
163+
description: The expression to obtain the version of the tool
164+
versions_prothint:
165+
- - ${task.process}:
166+
type: string
167+
description: The name of the process
168+
- prothint:
169+
type: string
170+
description: The name of the tool
171+
- prothint.py --version |& sed 's/prothint.py //1':
172+
type: eval
173+
description: The expression to obtain the version of the tool
174+
topics:
113175
versions:
114-
- versions.yml:
115-
type: file
116-
description: File containing software versions
117-
pattern: "versions.yml"
176+
- - ${task.process}:
177+
type: string
178+
description: The name of the process
179+
- braker3:
180+
type: string
181+
description: The name of the tool
182+
- braker.pl --version 2>/dev/null | sed 's/braker.pl version //':
183+
type: eval
184+
description: The expression to obtain the version of the tool
185+
- - ${task.process}:
186+
type: string
187+
description: The name of the process
188+
- augustus:
189+
type: string
190+
description: The name of the tool
191+
- augustus --version |& sed -n 's/AUGUSTUS (\(.*\)) is a gene .*/\1/p':
192+
type: eval
193+
description: The expression to obtain the version of the tool
194+
- - ${task.process}:
195+
type: string
196+
description: The name of the process
197+
- genemark-etp:
198+
type: string
199+
description: The name of the tool
200+
- gmetp.pl |& sed -n 's/ETP version \(.*\)/\1/p':
201+
type: eval
202+
description: The expression to obtain the version of the tool
203+
- - ${task.process}:
204+
type: string
205+
description: The name of the process
206+
- prothint:
207+
type: string
208+
description: The name of the tool
209+
- prothint.py --version |& sed 's/prothint.py //1':
210+
type: eval
211+
description: The expression to obtain the version of the tool
118212
authors:
119213
- "@kherronism"
120214
- "@GallVp"

‎modules/nf-core/braker3/tests/main.nf.test‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ nextflow_process {
1515
process {
1616
"""
1717
input[0] = [
18-
[ id:'test' ], // meta map
18+
[ id:'test' ],
1919
file('https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/genome.fa', checkIfExists: true)
2020
]
2121
input[1] = file('http://topaz.gatech.edu/GeneMark/Braker/RNAseq.bam', checkIfExists: true)
@@ -30,16 +30,16 @@ nextflow_process {
3030
then {
3131
assertAll(
3232
{ assert process.success },
33+
{ assert file(process.out.log[0][1]).text.contains('BRAKER RUN FINISHED') },
3334
{ assert snapshot(
3435
process.out.aa,
3536
process.out.cds,
3637
process.out.citations,
3738
process.out.gff3,
3839
process.out.gtf,
3940
process.out.hintsfile,
40-
process.out.versions,
41-
).match() },
42-
{ assert file(process.out.log[0][1]).text.contains('BRAKER RUN FINISHED') }
41+
process.out.findAll { key, val -> key.startsWith('versions') }
42+
).match() }
4343
)
4444
}
4545

@@ -53,7 +53,7 @@ nextflow_process {
5353
process {
5454
"""
5555
input[0] = [
56-
[ id:'test' ], // meta map
56+
[ id:'test' ],
5757
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
5858
]
5959
input[1] = []
@@ -68,7 +68,7 @@ nextflow_process {
6868
then {
6969
assertAll(
7070
{ assert process.success },
71-
{ assert snapshot(process.out).match() }
71+
{ assert snapshot(sanitizeOutput(process.out)).match() }
7272
)
7373
}
7474

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