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Merged
Aratz merged 3 commits into from
Mar 9, 2026
Merged

Patch release v3.0.1 #192

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edff12c
Remove if-statements from config
Aratz Mar 9, 2026
f52b607
Bump version to 3.0.1
Aratz Mar 9, 2026
662aefa
Apply prettier
Aratz Mar 9, 2026
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -23,4 +23,4 @@ template:
- fastqc
- multiqc
- igenomes
version: 3.0.0
version: 3.0.1
6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,12 @@
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).

## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09

### Enhancements & fixes

- Fix Issue #191 by @Aratz [#192](https://github.com/nf-core/pixelator/pull/183)

## [[3.0.0](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-02-23

### Changed
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10 changes: 0 additions & 10 deletions conf/modules.config
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Expand Up @@ -32,10 +32,6 @@ process {
pattern: '*.log'
]
]

if (params.pixelator_container) {
container = params.pixelator_container
}
}

withName: PIXELATOR_LIST_OPTIONS {
Expand All @@ -45,10 +41,4 @@ process {
withName: "CAT_FASTQ" {
publishDir = [ enabled: false ]
}

withName: "EXPERIMENT_SUMMARY" {
if (params.experiment_summary_container) {
container = params.experiment_summary_container
}
}
}
2 changes: 1 addition & 1 deletion modules/local/experiment_summary/main.nf
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Expand Up @@ -2,7 +2,7 @@ process EXPERIMENT_SUMMARY {
tag "${meta.id}"
label "process_medium"

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelatores:0.6.0'
: 'quay.io/pixelgen-technologies/pixelatores:0.6.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/list_options/main.nf
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Expand Up @@ -4,7 +4,7 @@ process PIXELATOR_LIST_OPTIONS {

// TODO: Add conda back
// conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/amplicon/main.nf
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Expand Up @@ -4,7 +4,7 @@ process PIXELATOR_PNA_AMPLICON {

// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/analysis/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PIXELATOR_PNA_ANALYSIS {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/collapse/main.nf
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Expand Up @@ -6,7 +6,7 @@ process PIXELATOR_PNA_COLLAPSE {

// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/combine_collapse/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PIXELATOR_PNA_COMBINE_COLLAPSE {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/demux/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PIXELATOR_PNA_DEMUX {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/denoise/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PIXELATOR_PNA_DENOISE {
// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/graph/main.nf
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Expand Up @@ -3,7 +3,7 @@ process PIXELATOR_PNA_GRAPH {
label 'process_high_memory'
label 'process_long'

container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion modules/local/pixelator/single-cell-pna/layout/main.nf
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Expand Up @@ -4,7 +4,7 @@ process PIXELATOR_PNA_LAYOUT {

// TODO: Add conda
// conda "bioconda::pixelator=0.18.2"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
: 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"

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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -357,7 +357,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.04.0'
version = '3.0.0'
version = '3.0.1'
doi = '10.1101/2023.06.05.543770'
}

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34 changes: 17 additions & 17 deletions ro-crate-metadata.json
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4 changes: 2 additions & 2 deletions tests/pna.nf.test.snap
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Expand Up @@ -109,7 +109,7 @@
"pixelator": "0.23.0"
},
"Workflow": {
"nf-core/pixelator": "v3.0.0"
"nf-core/pixelator": "v3.0.1"
}
}
],
Expand Down Expand Up @@ -154,7 +154,7 @@
"pixelator": "0.23.0"
},
"Workflow": {
"nf-core/pixelator": "v3.0.0"
"nf-core/pixelator": "v3.0.1"
}
},
[
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