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Swap repeatmasker to topics #12506

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45dd1a8
Swap repeatmasker to topics
SPPearce Aug 3, 2026
21e3582
Add linting
SPPearce Aug 3, 2026
2788d1b
Update modules/nf-core/repeatmasker/repeatmasker/environment.yml
SPPearce Sep 3, 2026
a5a1916
Merge branch 'master' into repeatmasker_topics
SPPearce Sep 3, 2026
d04b1db
Update modules/nf-core/repeatmasker/rmouttogff3/environment.yml
SPPearce Sep 5, 2026
4d145aa
Merge branch 'master' into repeatmasker_topics
SPPearce Sep 5, 2026
addde27
Merge branch 'master' into repeatmasker_topics
SPPearce Sep 7, 2026
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20 changes: 5 additions & 15 deletions modules/nf-core/repeatmasker/repeatmasker/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ process REPEATMASKER_REPEATMASKER {
path(lib)

output:
tuple val(meta), path("${prefix}.masked") , emit: masked
tuple val(meta), path("${prefix}.out") , emit: out
tuple val(meta), path("${prefix}.tbl") , emit: tbl
tuple val(meta), path("${prefix}.gff") , emit: gff , optional: true
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}.masked"), emit: masked
tuple val(meta), path("${prefix}.out") , emit: out
tuple val(meta), path("${prefix}.tbl") , emit: tbl
tuple val(meta), path("${prefix}.gff") , emit: gff, optional: true
tuple val("${task.process}"), val('repeatmasker'), eval("RepeatMasker -v | sed 's/RepeatMasker version //1'"), topic: versions, emit: versions_repeatmasker

when:
task.ext.when == null || task.ext.when
Expand All @@ -42,11 +42,6 @@ process REPEATMASKER_REPEATMASKER {
mv $prefix/${out_fasta}.out ${prefix}.out
mv $prefix/${out_fasta}.tbl ${prefix}.tbl
mv $prefix/${out_fasta}.out.gff ${prefix}.gff || echo "GFF is not produced"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1')
END_VERSIONS
"""

stub:
Expand All @@ -59,10 +54,5 @@ process REPEATMASKER_REPEATMASKER {
touch ${prefix}.out
touch ${prefix}.tbl
$touch_gff

cat <<-END_VERSIONS > versions.yml
"${task.process}":
repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1')
END_VERSIONS
"""
}
34 changes: 24 additions & 10 deletions modules/nf-core/repeatmasker/repeatmasker/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,11 @@
name: repeatmasker_repeatmasker
description: |
Screening DNA sequences for interspersed repeats and low complexity DNA sequences

keywords:
- genome
- annotation
- repeat
- mask

tools:
- repeatmasker:
description: |
Expand All @@ -16,7 +14,8 @@ tools:
homepage: "https://www.repeatmasker.org/"
documentation: "https://www.repeatmasker.org/webrepeatmaskerhelp.html"
tool_dev_url: "https://github.com/rmhubley/RepeatMasker"
licence: ["Open Software License v. 2.1"]
licence:
- "Open Software License v. 2.1"
identifier: biotools:repeatmasker

input:
Expand Down Expand Up @@ -83,17 +82,32 @@ output:
pattern: "*.{gff}"
ontologies:
- edam: http://edamontology.org/format_2305
versions_repeatmasker:
- - ${task.process}:
type: string
description: The name of the process
- repeatmasker:
type: string
description: The name of the tool
- RepeatMasker -v | sed 's/RepeatMasker version //1':
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- repeatmasker:
type: string
description: The name of the tool
- RepeatMasker -v | sed 's/RepeatMasker version //1':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@kherronism"
- "@gallvp"

maintainers:
- "@kherronism"
- "@gallvp"
23 changes: 5 additions & 18 deletions modules/nf-core/repeatmasker/repeatmasker/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -29,13 +29,7 @@ nextflow_process {
then {
assert process.success
assertAll(
{ assert snapshot(
process.out.masked,
process.out.out,
process.out.gff,
process.out.versions,
path(process.out.versions[0]).yaml
).match() },
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["tbl"])).match() },
{ assert file(process.out.tbl[0][1]).text.contains('run with rmblastn') }
)
}
Expand All @@ -61,13 +55,7 @@ nextflow_process {
then {
assert process.success
assertAll(
{ assert snapshot(
process.out.masked,
process.out.out,
process.out.gff,
process.out.versions,
path(process.out.versions[0]).yaml
).match() },
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["tbl"])).match() },
{ assert file(process.out.tbl[0][1]).text.contains('run with rmblastn') }
)
}
Expand Down Expand Up @@ -95,10 +83,9 @@ nextflow_process {

then {
assert process.success
assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match()
assertAll(
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}
Expand Down
176 changes: 79 additions & 97 deletions modules/nf-core/repeatmasker/repeatmasker/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,124 +1,107 @@
{
"sarscov2 - genome - fasta": {
"content": [
[
[
{
"id": "test"
},
"test.masked:md5,c0eb8dd958ce3b4b1fdc7fcb6b0d5161"
]
],
[
[
{
"id": "test"
},
"test.out:md5,8610cb2b8d87356bf2ab0a895c065752"
]
],
[
[
{
"id": "test"
},
"test.gff:md5,289cdcae609a8c450a20080107ea6351"
]
],
[
"versions.yml:md5,1386abb5112b809c321da8ddc598c573"
],
{
"REPEATMASKER_REPEATMASKER": {
"repeatmasker": "4.1.5"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-06-09T14:28:28.754319473"
},
"sarscov2 - genome - fasta.gz": {
"content": [
[
[
{
"id": "test"
},
"test.masked:md5,c0eb8dd958ce3b4b1fdc7fcb6b0d5161"
]
],
[
[
{
"id": "test"
},
"test.out:md5,8610cb2b8d87356bf2ab0a895c065752"
]
],
[
[
{
"id": "test"
},
"test.gff:md5,289cdcae609a8c450a20080107ea6351"
"gff": [
[
{
"id": "test"
},
"test.gff:md5,289cdcae609a8c450a20080107ea6351"
]
],
"masked": [
[
{
"id": "test"
},
"test.masked:md5,c0eb8dd958ce3b4b1fdc7fcb6b0d5161"
]
],
"out": [
[
{
"id": "test"
},
"test.out:md5,8610cb2b8d87356bf2ab0a895c065752"
]
],
"tbl": [
[
{
"id": "test"
},
"test.tbl"
]
],
"versions_repeatmasker": [
[
"REPEATMASKER_REPEATMASKER",
"repeatmasker",
"4.1.5"
]
]
],
[
"versions.yml:md5,1386abb5112b809c321da8ddc598c573"
],
{
"REPEATMASKER_REPEATMASKER": {
"repeatmasker": "4.1.5"
}
}
],
"timestamp": "2026-08-03T12:53:48.353518664",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-06-09T14:29:16.280370801"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"sarscov2 - genome - fasta - stub": {
"sarscov2 - genome - fasta.gz": {
"content": [
{
"0": [
"gff": [
[
{
"id": "test"
},
"test.masked:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.gff:md5,289cdcae609a8c450a20080107ea6351"
]
],
"1": [
"masked": [
[
{
"id": "test"
},
"test.out:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.masked:md5,c0eb8dd958ce3b4b1fdc7fcb6b0d5161"
]
],
"2": [
"out": [
[
{
"id": "test"
},
"test.tbl:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.out:md5,8610cb2b8d87356bf2ab0a895c065752"
]
],
"3": [
"tbl": [
[
{
"id": "test"
},
"test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.tbl"
]
],
"4": [
"versions.yml:md5,1386abb5112b809c321da8ddc598c573"
],
"versions_repeatmasker": [
[
"REPEATMASKER_REPEATMASKER",
"repeatmasker",
"4.1.5"
]
]
}
],
"timestamp": "2026-08-03T12:54:10.486241826",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"sarscov2 - genome - fasta - stub": {
"content": [
{
"gff": [
[
{
Expand Down Expand Up @@ -151,20 +134,19 @@
"test.tbl:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,1386abb5112b809c321da8ddc598c573"
"versions_repeatmasker": [
[
"REPEATMASKER_REPEATMASKER",
"repeatmasker",
"4.1.5"
]
]
},
{
"REPEATMASKER_REPEATMASKER": {
"repeatmasker": "4.1.5"
}
}
],
"timestamp": "2026-08-03T12:54:16.336690987",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-06-09T14:59:31.7951404"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}
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