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migrate toulligqc to topic versions #9750

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12 changes: 1 addition & 11 deletions modules/nf-core/toulligqc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ process TOULLIGQC {
tuple val(meta), path("*/*.html") , emit: report_html, optional: true
tuple val(meta), path("*/images/*.html") , emit: plots_html
tuple val(meta), path("*/images/plotly.min.js") , emit: plotly_js
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('toulligqc'), eval('toulligqc --version'), emit: versions_toulligqc, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -35,11 +35,6 @@ process TOULLIGQC {
$input_file \\
--output-directory ${prefix} \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
toulligqc: \$(toulligqc --version)
END_VERSIONS
"""

stub:
Expand All @@ -54,10 +49,5 @@ process TOULLIGQC {
touch ${prefix}/images/PHRED_score_density_distribution.html
touch ${prefix}/images/Read_count_histogram.html
touch ${prefix}/images/plotly.min.js

cat <<-END_VERSIONS > versions.yml
"${task.process}":
toulligqc: \$(toulligqc --version)
END_VERSIONS
"""
}
27 changes: 21 additions & 6 deletions modules/nf-core/toulligqc/meta.yml
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Expand Up @@ -71,13 +71,28 @@ output:
description: Plots emitted from toulligqc
pattern: "plotly.min.js"
ontologies: []
versions_toulligqc:
- - ${task.process}:
type: string
description: Name of the process
- toulligqc:
type: string
description: Name of the tool
- toulligqc --version:
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: Name of the process
- toulligqc:
type: string
description: Name of the tool
- toulligqc --version:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@Salome-Brunon"
maintainers:
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/toulligqc/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("toulligqc_versions_sequencing_summary") },
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("toulligqc_versions_sequencing_summary") },
{ assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..74]).match() },
{ assert process.out.report_html[0][1] ==~ ".*/report.html"}
)
Expand All @@ -47,7 +47,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("toulligqc_versions_sequencing_summary_barcodes") },
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("toulligqc_versions_sequencing_summary_barcodes") },
{ assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..74]).match() },
{ assert process.out.report_html[0][1] ==~ ".*/report.html"}
)
Expand All @@ -70,7 +70,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("toulligqc_versions_fastq") },
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("toulligqc_versions_fastq") },
{ assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..67]).match() },
{ assert process.out.report_html[0][1] ==~ ".*/report.html"}
)
Expand All @@ -93,7 +93,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("toulligqc_versions_bam") },
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("toulligqc_versions_bam") },
{ assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..74]).match() },
{ assert process.out.report_html[0][1] ==~ ".*/report.html"}
)
Expand All @@ -118,7 +118,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match("toulligqc_versions_stub") }
{ assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("toulligqc_versions_stub") }
)
}
}
Expand Down
90 changes: 60 additions & 30 deletions modules/nf-core/toulligqc/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -76,15 +76,21 @@
},
"toulligqc_versions_sequencing_summary_barcodes": {
"content": [
[
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
{
"versions_toulligqc": [
[
"TOULLIGQC",
"toulligqc",
"2.7.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-04T13:34:41.406227395"
"timestamp": "2026-01-22T14:29:55.724424127"
},
"sarscov2 - nanopore sequencing_summary + barcodes": {
"content": [
Expand Down Expand Up @@ -163,15 +169,21 @@
},
"toulligqc_versions_bam": {
"content": [
[
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
{
"versions_toulligqc": [
[
"TOULLIGQC",
"toulligqc",
"2.7.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-04T13:36:09.017460415"
"timestamp": "2026-01-22T14:30:18.794347511"
},
"sarscov2 - nanopore bam": {
"content": [
Expand Down Expand Up @@ -250,39 +262,57 @@
},
"toulligqc_versions_stub": {
"content": [
[
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
{
"versions_toulligqc": [
[
"TOULLIGQC",
"toulligqc",
"2.7.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-04T13:37:17.104275439"
"timestamp": "2026-01-22T14:30:26.839592056"
},
"toulligqc_versions_fastq": {
"content": [
[
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
{
"versions_toulligqc": [
[
"TOULLIGQC",
"toulligqc",
"2.7.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-04T13:35:56.755396126"
"timestamp": "2026-01-22T14:30:07.213424763"
},
"toulligqc_versions_sequencing_summary": {
"content": [
[
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
{
"versions_toulligqc": [
[
"TOULLIGQC",
"toulligqc",
"2.7.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-04T13:34:26.320114673"
"timestamp": "2026-01-22T14:29:44.055859712"
},
"sarscov2 - nanopore fastq": {
"content": [
Expand Down
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