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Merged
johandahlberg merged 9 commits into from
Jun 4, 2026
Merged

Release 4.1.2 #223

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106319f
Bump version to 4.2.0dev
Aratz May 29, 2026
ccf598f
Merge pull request #220 from Aratz/dev
Aratz May 29, 2026
baa3ff9
Update pixelator to 0.28.0
johandahlberg Jun 3, 2026
8d53a46
Clearer changelog
johandahlberg Jun 4, 2026
4b870d0
Set version target in nextflow.config
johandahlberg Jun 4, 2026
d1271a0
Update snapshots with new version targets
johandahlberg Jun 4, 2026
9741322
Merge pull request #221 from nf-core/update-to-pixelator-0.28.0
johandahlberg Jun 4, 2026
de94c7a
Bump version to 4.1.2
johandahlberg Jun 4, 2026
b3b1183
Merge pull request #222 from nf-core/prerelease-4.1.2
johandahlberg Jun 4, 2026
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -24,4 +24,4 @@ template:
- fastqc
- multiqc
- igenomes
version: 4.1.1
version: 4.1.2
13 changes: 13 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,19 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [[4.1.2](https://github.com/nf-core/pixelator/releases/tag/4.1.2)] - 2026-06-04

### Enhancements & fixes

- Update pixelator container to 0.28.0. This fixes a major performance regression
in the graph step, which caused very high memory usage. By @johandahlberg [#221](https://github.com/nf-core/pixelator/pull/221)

### Software dependencies

| Dependency | Old version | New version |
| ----------- | ----------- | ----------- |
| `pixelator` | 0.27.2 | 0.28.0 |

## [[4.1.1](https://github.com/nf-core/pixelator/releases/tag/4.1.1)] - 2026-05-29

### Enhancements & fixes
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4 changes: 2 additions & 2 deletions modules/local/pixelator/amplicon/main.nf
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Expand Up @@ -5,8 +5,8 @@ process PIXELATOR_AMPLICON {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(reads, arity: '1..*')
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6 changes: 3 additions & 3 deletions modules/local/pixelator/amplicon/tests/main.nf.test.snap
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Expand Up @@ -60,7 +60,7 @@
[
"PIXELATOR_AMPLICON",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"amplicon": [
Expand Down Expand Up @@ -111,7 +111,7 @@
[
"PIXELATOR_AMPLICON",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
Expand Down Expand Up @@ -140,7 +140,7 @@
[
"PIXELATOR_AMPLICON",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
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4 changes: 2 additions & 2 deletions modules/local/pixelator/analysis/main.nf
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Expand Up @@ -6,8 +6,8 @@ process PIXELATOR_ANALYSIS {
// conda "bioconda::pixelator=0.18.2"

container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(data)
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6 changes: 3 additions & 3 deletions modules/local/pixelator/analysis/tests/main.nf.test.snap
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Expand Up @@ -17,7 +17,7 @@
[
"PIXELATOR_ANALYSIS",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -103,7 +103,7 @@
[
"PIXELATOR_ANALYSIS",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"all_results": [
Expand Down Expand Up @@ -169,7 +169,7 @@
[
"PIXELATOR_ANALYSIS",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
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4 changes: 2 additions & 2 deletions modules/local/pixelator/collapse/main.nf
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Expand Up @@ -7,8 +7,8 @@ process PIXELATOR_COLLAPSE {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(reads), path(panel_file), val(panel), val(design)
Expand Down
6 changes: 3 additions & 3 deletions modules/local/pixelator/collapse/tests/main.nf.test.snap
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Expand Up @@ -17,7 +17,7 @@
[
"PIXELATOR_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -92,7 +92,7 @@
[
"PIXELATOR_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"collapsed": [
Expand Down Expand Up @@ -147,7 +147,7 @@
[
"PIXELATOR_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
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4 changes: 2 additions & 2 deletions modules/local/pixelator/combine_collapse/main.nf
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Expand Up @@ -6,8 +6,8 @@ process PIXELATOR_COMBINE_COLLAPSE {
// conda "bioconda::pixelator=0.18.2"

container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(parquet_files, stageAs: "parquet/*"), path(json_report_files, stageAs: "reports/*")
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6 changes: 3 additions & 3 deletions modules/local/pixelator/combine_collapse/tests/main.nf.test.snap
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Expand Up @@ -16,7 +16,7 @@
[
"PIXELATOR_COMBINE_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -87,7 +87,7 @@
[
"PIXELATOR_COMBINE_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"log": [
Expand Down Expand Up @@ -138,7 +138,7 @@
[
"PIXELATOR_COMBINE_COLLAPSE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
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4 changes: 2 additions & 2 deletions modules/local/pixelator/demux/main.nf
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Expand Up @@ -6,8 +6,8 @@ process PIXELATOR_DEMUX {
// conda "bioconda::pixelator=0.18.2"

container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(reads), path(panel_file), val(panel), val(design)
Expand Down
8 changes: 4 additions & 4 deletions modules/local/pixelator/demux/tests/main.nf.test.snap
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Expand Up @@ -20,7 +20,7 @@
[
"PIXELATOR_DEMUX",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -119,7 +119,7 @@
[
"PIXELATOR_DEMUX",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"demuxed": [
Expand Down Expand Up @@ -195,7 +195,7 @@
[
"PIXELATOR_DEMUX",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
Expand Down Expand Up @@ -241,7 +241,7 @@
[
"PIXELATOR_DEMUX",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
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4 changes: 2 additions & 2 deletions modules/local/pixelator/denoise/main.nf
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Expand Up @@ -6,8 +6,8 @@ process PIXELATOR_DENOISE {
// conda "bioconda::pixelator=0.18.2"

container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(data)
Expand Down
6 changes: 3 additions & 3 deletions modules/local/pixelator/denoise/tests/main.nf.test.snap
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Expand Up @@ -16,7 +16,7 @@
[
"PIXELATOR_DENOISE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -102,7 +102,7 @@
[
"PIXELATOR_DENOISE",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"all_results": [
Expand Down Expand Up @@ -168,7 +168,7 @@
[
"PIXELATOR_DENOISE",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
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4 changes: 2 additions & 2 deletions modules/local/pixelator/graph/main.nf
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Expand Up @@ -4,8 +4,8 @@ process PIXELATOR_GRAPH {
label 'process_long'

container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(edge_list), path(panel_file), val(panel)
Expand Down
6 changes: 3 additions & 3 deletions modules/local/pixelator/graph/tests/main.nf.test.snap
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Expand Up @@ -75,7 +75,7 @@
[
"PIXELATOR_GRAPH",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"all_results": [
Expand Down Expand Up @@ -141,7 +141,7 @@
[
"PIXELATOR_GRAPH",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
Expand Down Expand Up @@ -170,7 +170,7 @@
[
"PIXELATOR_GRAPH",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down
4 changes: 2 additions & 2 deletions modules/local/pixelator/layout/main.nf
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Expand Up @@ -5,8 +5,8 @@ process PIXELATOR_LAYOUT {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(data)
Expand Down
6 changes: 3 additions & 3 deletions modules/local/pixelator/layout/tests/main.nf.test.snap
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Expand Up @@ -17,7 +17,7 @@
[
"PIXELATOR_LAYOUT",
"pixelator",
"0.27.2"
"0.28.0"
]
]
],
Expand Down Expand Up @@ -103,7 +103,7 @@
[
"PIXELATOR_LAYOUT",
"pixelator",
"0.27.2"
"0.28.0"
]
],
"all_results": [
Expand Down Expand Up @@ -169,7 +169,7 @@
[
"PIXELATOR_LAYOUT",
"pixelator",
"0.27.2"
"0.28.0"
]
]
}
Expand Down
4 changes: 2 additions & 2 deletions modules/local/pixelator/list_options/main.nf
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Expand Up @@ -5,8 +5,8 @@ process PIXELATOR_LIST_OPTIONS {
// TODO: Add conda back
// conda "${moduleDir}/environment.yml"
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

output:
path "design_options.txt", emit: designs
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4 changes: 2 additions & 2 deletions modules/local/pixelator/sample_calling/main.nf
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Expand Up @@ -5,8 +5,8 @@ process PIXELATOR_SAMPLE_CALLING {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
? 'quay.io/pixelgen-technologies/pixelator:0.28.0'
: 'quay.io/pixelgen-technologies/pixelator:0.28.0'}"

input:
tuple val(meta), path(data), path(samplesheet)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/pixelator/sample_calling/tests/main.nf.test.snap
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Expand Up @@ -111,7 +111,7 @@
]
],
"6": [
"versions.yml:md5,b92ce490993aa65332cf3e1fce6c4ff7"
"versions.yml:md5,caecdbbf67cdc742583ac0658769573d"
],
"all_results": [
[
Expand Down Expand Up @@ -181,7 +181,7 @@
]
],
"versions": [
"versions.yml:md5,b92ce490993aa65332cf3e1fce6c4ff7"
"versions.yml:md5,caecdbbf67cdc742583ac0658769573d"
]
}
],
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -375,7 +375,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.10.4'
version = '4.1.1'
version = '4.1.2'
doi = '10.1101/2023.06.05.543770'
}

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