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migrate shovill module to topic versions #9748

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migrate shovill module to topic versions #9748

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90951a6
migrate shovill module to topic versions
eit-maxlcummins Jan 22, 2026
f802177
add to authorship
eit-maxlcummins Jan 22, 2026
d4ed596
Merge branch 'master' into shovill_topic_versions
eit-maxlcummins Jan 22, 2026
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7 changes: 1 addition & 6 deletions modules/nf-core/shovill/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process SHOVILL {
tuple val(meta), path("shovill.log") , emit: log
tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
tuple val(meta), path("contigs.{fastg,gfa,LastGraph}") , optional:true, emit: gfa
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('shovill'), eval('shovill --version 2>&1 | sed "s/^.*shovill //"'), emit: versions_shovill, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -33,10 +33,5 @@ process SHOVILL {
--ram $memory \\
--outdir ./ \\
--force

cat <<-END_VERSIONS > versions.yml
"${task.process}":
shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
END_VERSIONS
"""
}
28 changes: 22 additions & 6 deletions modules/nf-core/shovill/meta.yml
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Expand Up @@ -79,14 +79,30 @@ output:
pattern: "contigs.{fastg,gfa,LastGraph}"
ontologies:
- edam: http://edamontology.org/format_3975 # GFA 1
versions_shovill:
- - "${task.process}":
type: string
description: The name of the process
- shovill:
type: string
description: The name of the tool
- shovill --version 2>&1 | sed "s/^.*shovill //":
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
- shovill:
type: string
description: The name of the tool
- shovill --version 2>&1 | sed "s/^.*shovill //":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@rpetit3"
- "@eit-maxlcummins"
maintainers:
- "@rpetit3"
8 changes: 4 additions & 4 deletions modules/nf-core/shovill/tests/main.nf.test
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Expand Up @@ -25,7 +25,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(path(process.out.versions.get(0))).match() },
{ assert process.out.findAll { key, val -> key.startsWith('versions') }},
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@SPPearce SPPearce Jan 23, 2026

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This needs to be within the snapshot, as it is not currently checking anything.

{ assert process.out.raw_contigs.size() == 1 },
{ assert path(process.out.gfa.get(0).get(1)).readLines().any { it.contains("S") } },
{ assert path(process.out.gfa.get(0).get(1)).readLines().any { it.contains("KC") } },
Expand Down Expand Up @@ -54,7 +54,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(path(process.out.versions.get(0))).match() },
{ assert process.out.findAll { key, val -> key.startsWith('versions') }},
{ assert process.out.raw_contigs.size() == 1 },
{ assert process.out.raw_contigs.get(0).get(1) ==~ ".*skesa.fasta" },
{ assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains(">Contig_1") } },
Expand All @@ -79,7 +79,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(path(process.out.versions.get(0))).match() },
{ assert process.out.findAll { key, val -> key.startsWith('versions') }},
{ assert process.out.raw_contigs.size() == 1 },
{ assert process.out.raw_contigs.get(0).get(1) ==~ ".*megahit.fasta" },
{ assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains("pilon") } }
Expand All @@ -103,7 +103,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(path(process.out.versions.get(0))).match() },
{ assert process.out.findAll { key, val -> key.startsWith('versions') }},
{ assert process.out.raw_contigs.size() == 1 },
{ assert process.out.raw_contigs.get(0).get(1) ==~ ".*velvet.fasta" },
{ assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains("pilon") } }
Expand Down
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