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Update to topic phispy #12576

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aceaa25
Update to topic
LouisLeNezet Aug 4, 2026
81d6424
Fix test and environment
LouisLeNezet Aug 4, 2026
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2 changes: 2 additions & 0 deletions modules/nf-core/phispy/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,5 @@ channels:
dependencies:
- bioconda::phispy=4.2.21
- conda-forge::biopython=1.81
- conda-forge::python=3.10.5
- conda-forge::setuptools=63.3.0
43 changes: 17 additions & 26 deletions modules/nf-core/phispy/main.nf
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Expand Up @@ -14,15 +14,15 @@ process PHISPY {
tuple val(meta), path("${prefix}.tsv") , emit: coordinates
tuple val(meta), path("${prefix}.gb*") , emit: gbk
tuple val(meta), path("${prefix}.log") , emit: log
tuple val(meta), path("${prefix}_prophage_information.tsv"), optional:true, emit: information
tuple val(meta), path("${prefix}_bacteria.fasta") , optional:true, emit: bacteria_fasta
tuple val(meta), path("${prefix}_bacteria.gbk") , optional:true, emit: bacteria_gbk
tuple val(meta), path("${prefix}_phage.fasta") , optional:true, emit: phage_fasta
tuple val(meta), path("${prefix}_phage.gbk") , optional:true, emit: phage_gbk
tuple val(meta), path("${prefix}_prophage.gff3") , optional:true, emit: prophage_gff
tuple val(meta), path("${prefix}_prophage.tbl") , optional:true, emit: prophage_tbl
tuple val(meta), path("${prefix}_prophage.tsv") , optional:true, emit: prophage_tsv
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}_prophage_information.tsv"), emit: information , optional:true
tuple val(meta), path("${prefix}_bacteria.fasta") , emit: bacteria_fasta, optional:true
tuple val(meta), path("${prefix}_bacteria.gbk") , emit: bacteria_gbk , optional:true
tuple val(meta), path("${prefix}_phage.fasta") , emit: phage_fasta , optional:true
tuple val(meta), path("${prefix}_phage.gbk") , emit: phage_gbk , optional:true
tuple val(meta), path("${prefix}_prophage.gff3") , emit: prophage_gff , optional:true
tuple val(meta), path("${prefix}_prophage.tbl") , emit: prophage_tbl , optional:true
tuple val(meta), path("${prefix}_prophage.tsv") , emit: prophage_tsv , optional:true
tuple val("${task.process}"), val('phispy'), eval('PhiSpy.py --version 2>&1'), topic: versions, emit: versions_phispy

when:
task.ext.when == null || task.ext.when
Expand All @@ -33,35 +33,31 @@ process PHISPY {
// Extract GBK file extension, i.e. .gbff, .gbk.gz
gbk_extension = gbk.getName() - gbk.getSimpleName()

if ("$gbk" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
if ("${gbk}" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

"""
PhiSpy.py \\
$args \\
--threads $task.cpus \\
-p $prefix \\
${args} \\
--threads ${task.cpus} \\
-p ${prefix} \\
-o . \\
$gbk
${gbk}

mv ${prefix}_prophage_coordinates.tsv ${prefix}.tsv
mv ${prefix}_${gbk} ${prefix}${gbk_extension}
mv ${prefix}_phispy.log ${prefix}.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
PhiSpy: \$(echo \$(PhiSpy.py --version 2>&1))
END_VERSIONS
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
gbk_extension = gbk.getName() - gbk.getSimpleName()
gbl_create_cmd = gbk_extension.endsWith(".gz") ? 'echo "" | gzip >' : "touch"

if ("$gbk" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
if ("${gbk}" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

"""
touch ${prefix}.tsv
touch ${prefix}${gbk_extension}
${gbl_create_cmd} ${prefix}${gbk_extension}
touch ${prefix}.log
touch ${prefix}_prophage_information.tsv
touch ${prefix}_bacteria.fasta
Expand All @@ -71,10 +67,5 @@ process PHISPY {
touch ${prefix}_prophage.gff3
touch ${prefix}_prophage.tbl
touch ${prefix}_prophage.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
PhiSpy: \$(echo \$(PhiSpy.py --version 2>&1))
END_VERSIONS
"""
}
32 changes: 24 additions & 8 deletions modules/nf-core/phispy/meta.yml
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@@ -1,4 +1,3 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "phispy"
description: Predict prophages in bacterial genomes
keywords:
Expand All @@ -15,7 +14,8 @@ tools:
documentation: "https://github.com/linsalrob/PhiSpy/blob/master/README.md"
tool_dev_url: "https://github.com/linsalrob/PhiSpy/"
doi: "10.1093/nar/gks406"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -163,13 +163,29 @@ output:
pattern: "*.{tsv}"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV
versions_phispy:
- - ${task.process}:
type: string
description: The name of the process
- phispy:
type: string
description: The name of the tool
- PhiSpy.py --version 2>&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
- phispy:
type: string
description: The name of the tool
- PhiSpy.py --version 2>&1:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@jvfe"
maintainers:
Expand Down
48 changes: 14 additions & 34 deletions modules/nf-core/phispy/tests/main.nf.test
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Expand Up @@ -15,7 +15,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ id:'test' ],
file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true )
]
"""
Expand All @@ -25,25 +25,20 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{
with(process.out.log[0]) {
assert path(get(1)).text.contains('NZ_CP069563.1')
assert path(get(1)).text.contains('91')
assert path(get(1)).text.contains('Kept')
}
},
{
with(process.out.coordinates[0]) {
assert path(get(1)).text.contains('NZ_CP069563.1')
assert path(get(1)).text.contains('pp1')
assert path(get(1)).text.contains('Longest Repeat flanking phage and within 2000 bp')
}
},
{ with(process.out.log[0]) {
assert path(get(1)).text.contains('NZ_CP069563.1')
assert path(get(1)).text.contains('91')
assert path(get(1)).text.contains('Kept')
}},
{ with(process.out.coordinates[0]) {
assert path(get(1)).text.contains('NZ_CP069563.1')
assert path(get(1)).text.contains('pp1')
assert path(get(1)).text.contains('Longest Repeat flanking phage and within 2000 bp')
}},
{ assert path(process.out.gbk[0][1]).linesGzip.toString().contains('5150703 bp') },
{ assert snapshot(process.out.versions).match() }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["log", "coordinates", "gbk"])).match() }
)
}

}

test("bacteroides_fragilis - gbff - stub") {
Expand All @@ -54,7 +49,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ id:'test' ],
file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true )
]
"""
Expand All @@ -64,24 +59,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert path(process.out.gbk[0][1]).exists() },
{ assert snapshot(
process.out.coordinates,
process.out.log,
process.out.information,
process.out.bacteria_fasta,
process.out.bacteria_gbk,
process.out.phage_fasta,
process.out.phage_gbk,
process.out.prophage_gff,
process.out.prophage_tbl,
process.out.prophage_tsv,
process.out.versions
).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

}
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