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Merged
SPPearce merged 1 commit into from
Aug 10, 2026
Merged

Update to topic proovframe #12615

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2 changes: 1 addition & 1 deletion modules/nf-core/proovframe/fix/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::proovframe=0.9.7"
- bioconda::proovframe=0.9.7
12 changes: 1 addition & 11 deletions modules/nf-core/proovframe/fix/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process PROOVFRAME_FIX {

output:
tuple val(meta), path("*.fa"), emit: out_fa
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('proovframe'), eval("proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//'"), topic: versions, emit: versions_proovframe

when:
task.ext.when == null || task.ext.when
Expand All @@ -28,21 +28,11 @@ process PROOVFRAME_FIX {
-o ${prefix}.fa \\
${fa} \\
${tsv}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*')
END_VERSIONS
"""
}
38 changes: 26 additions & 12 deletions modules/nf-core/proovframe/fix/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "proovframe_fix"
description: frame-shift correction for long read (meta)genomics - fix frameshifts
in reads
description: frame-shift correction for long read (meta)genomics - fix frameshifts in reads
keywords:
- frame-shift correction
- long-read sequencing
Expand All @@ -13,7 +11,8 @@ tools:
documentation: "https://github.com/thackl/proovframe"
tool_dev_url: "https://github.com/thackl/proovframe"
doi: "10.1101/2021.08.23.457338"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:proovframe

input:
Expand All @@ -34,8 +33,7 @@ input:
e.g. [ id:'test' ]
- tsv:
type: file
description: "Output TSV file from proovframe/map with the frameshift-aware
protein to read alignments from proovframe/map"
description: "Output TSV file from proovframe/map with the frameshift-aware protein to read alignments from proovframe/map"
pattern: "*.{tsv}"

ontologies:
Expand All @@ -52,13 +50,29 @@ output:
description: "Result FASTA with fixed frameshift reads"
pattern: "*.{fa}"
ontologies: []
versions_proovframe:
- - ${task.process}:
type: string
description: The name of the process
- proovframe:
type: string
description: The name of the tool
- proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//':
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
- proovframe:
type: string
description: The name of the tool
- proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@mcarbajo"
- "@vagkaratzas"
Expand Down
18 changes: 6 additions & 12 deletions modules/nf-core/proovframe/fix/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,11 +16,11 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'fa', single_end:false ], // meta map
[ id:'fa' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [
[ id:'fa', single_end:false ], // meta map
[ id:'fa' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
]
input[2] = [[:], []]
Expand All @@ -30,12 +30,11 @@ nextflow_process {
}

test("test - fa_tsv") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = PROOVFRAME_MAP.out.tsv
Expand All @@ -46,21 +45,18 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

test("test - faa_fasta - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = PROOVFRAME_MAP.out.tsv
Expand All @@ -71,10 +67,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

}
58 changes: 20 additions & 38 deletions modules/nf-core/proovframe/fix/tests/main.nf.test.snap
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Expand Up @@ -2,71 +2,53 @@
"test - fa_tsv": {
"content": [
{
"0": [
"out_fa": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test.fa:md5,83eccce28287b72c524ea022996d465f"
]
],
"1": [
"versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4"
],
"out_fa": [
"versions_proovframe": [
[
{
"id": "test",
"single_end": false
},
"test.fa:md5,83eccce28287b72c524ea022996d465f"
"PROOVFRAME_FIX",
"proovframe",
"0.9.7"
]
],
"versions": [
"versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4"
]
}
],
"timestamp": "2026-08-07T11:34:34.512092731",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-11-06T16:40:56.201526311"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"test - faa_fasta - stub": {
"content": [
{
"0": [
"out_fa": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4"
],
"out_fa": [
"versions_proovframe": [
[
{
"id": "test",
"single_end": false
},
"test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
"PROOVFRAME_FIX",
"proovframe",
"0.9.7"
]
],
"versions": [
"versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4"
]
}
],
"timestamp": "2026-08-07T11:34:41.56607229",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-11-06T16:44:04.101218224"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/proovframe/map/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::proovframe=0.9.7"
- bioconda::proovframe=0.9.7
12 changes: 1 addition & 11 deletions modules/nf-core/proovframe/map/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process PROOVFRAME_MAP {

output:
tuple val(meta), path("*.tsv"), emit: tsv
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('proovframe'), eval("proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//'"), topic: versions, emit: versions_proovframe

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,21 +32,11 @@ process PROOVFRAME_MAP {
${db_type} \\
-o ${prefix}.tsv \\
${fasta}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*')
END_VERSIONS
"""
}
37 changes: 25 additions & 12 deletions modules/nf-core/proovframe/map/meta.yml
View file
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "proovframe_map"
description: frame-shift correction for long read (meta)genomics - maps proteins to
reads
description: frame-shift correction for long read (meta)genomics - maps proteins to reads
keywords:
- frame-shift correction
- long-read sequencing
Expand All @@ -13,7 +11,8 @@ tools:
documentation: "https://github.com/thackl/proovframe"
tool_dev_url: "https://github.com/thackl/proovframe"
doi: "10.1101/2021.08.23.457338"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:proovframe

input:
Expand All @@ -34,8 +33,7 @@ input:
e.g. `[ id:'sample1', single_end:false ]`
- faa:
type: file
description: A proteome fasta file to create a database of guide protein sequences
from
description: A proteome fasta file to create a database of guide protein sequences from
pattern: "*.{faa,fasta,fa}"
ontologies: []
- - meta3:
Expand All @@ -61,13 +59,28 @@ output:
pattern: "*.{tsv}"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV
versions_proovframe:
- - ${task.process}:
type: string
description: The name of the process
- proovframe:
type: string
description: The name of the tool
- proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//':
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
- proovframe:
type: string
description: The name of the tool
- proovframe 2>&1 | sed '/proovframe-v/!d;s/proovframe-v//;s/ .*//':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@manuelcarbajo"
Expand Down
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