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Merge pull request #217 from Aratz/update_pixelator_0.27.2
Update pixelator 0.27.2
2 parents 561ccbf + 34d6fe8 commit 6160e77

39 files changed

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‎CHANGELOG.md‎

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@@ -8,6 +8,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Enhancements & fixes
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- Improve documentation by @Aratz [#216](https://github.com/nf-core/pixelator/pull/216)
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- Update pixelator by @Aratz [#217](https://github.com/nf-core/pixelator/pull/217)
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### Software dependencies
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| Dependency | Old version | New version |
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| ----------- | ----------- | ----------- |
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| `pixelator` | 0.27.1 | 0.27.2 |
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## [[4.1.0](https://github.com/nf-core/pixelator/releases/tag/4.1.0)] - 2026-05-28
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‎README.md‎

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@@ -62,9 +62,9 @@ For hashed PNA data (Proxiome kit v2), the samplesheet will look as follows:
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```csv
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pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,2,sample2,s2,case,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool2,1,sample3,s3,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool2_R1_001.fastq.gz,pool2_R2_001.fastq.gz
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```
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> [!NOTE]

‎assets/example_samplesheet_proxiome_v2.csv‎

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pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz

‎assets/schema_input.json‎

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"const": "proxiome-v2"
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},
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"panel": {
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"const": "proxiome-v2-immuno-155-v1.0"
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"pattern": "^proxiome-v2-"
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}
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},
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"required": ["design", "panel"]
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},
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"then": {
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"required": ["pool", "hash_index"],
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"errorMessage": "The `pool` and `hash_index` columns are required for `proxiome-v2` design with panel `proxiome-v2-immuno-155-v1.0`."
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"errorMessage": "The `pool` and `hash_index` columns are required for `proxiome-v2` design with a `proxiome-v2` panel."
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}
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}
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],

‎docs/usage.md‎

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```csv
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pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool2,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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pool2,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_R1_001.fastq.gz,pool1_R2_001.fastq.gz
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```
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### Multiple runs of the same sample
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```csv title="samplesheet.csv"
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pool,hash_index,sample,sample_alias,condition,design,panel,fastq_1,fastq_2
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v1.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz
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pool1,1,sample1,s1,control,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_run1_R1_001.fastq.gz,pool1_run1_R2_001.fastq.gz
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pool1,2,sample2,s2,treatment,proxiome-v2,proxiome-v2-immuno-155-v2.0,pool1_run2_R1_001.fastq.gz,pool1_run2_R2_001.fastq.gz
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```
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### Relative paths

‎modules/local/experiment_summary/tests/main.nf.test‎

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"""
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input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ]
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input[1] = [
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[id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ],
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[id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ],
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[
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'amplicon', 'amplicon',
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],
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"""
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input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_proxiome_v2.csv', checkIfExists: true) ]
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input[1] = [
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[id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ],
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[id:'all', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ],
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[
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'amplicon', 'amplicon', 'amplicon', 'amplicon',
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'demux', 'demux', 'demux', 'demux',

‎modules/local/pixelator/amplicon/main.nf‎

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// TODO: Add conda
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// conda "bioconda::pixelator=0.18.2"
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container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'quay.io/pixelgen-technologies/pixelator:0.27.1'
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: 'quay.io/pixelgen-technologies/pixelator:0.27.1'}"
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? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
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: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
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input:
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tuple val(meta), path(reads, arity: '1..*')

‎modules/local/pixelator/amplicon/tests/main.nf.test‎

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process {
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"""
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input[0] = [
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[ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ],
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[ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ],
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[
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file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true)
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process {
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"""
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input[0] = [
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[ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v1.0', technology:'proxiome-v2' ],
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[ id:'pool1', design:'proxiome-v2', panel:'proxiome-v2-immuno-155-v2.0', technology:'proxiome-v2' ],
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[
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file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R1.fastq.gz', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'testdata/pna/fastq/pool1_R2.fastq.gz', checkIfExists: true)

‎modules/local/pixelator/amplicon/tests/main.nf.test.snap‎

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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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[
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"PIXELATOR_AMPLICON",
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"pixelator",
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"0.27.1"
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"0.27.2"
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]
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],
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"amplicon": [
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[
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.amplicon.fq.zst:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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{
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"id": "pool1",
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"design": "proxiome-v2",
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"panel": "proxiome-v2-immuno-155-v1.0",
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"panel": "proxiome-v2-immuno-155-v2.0",
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"technology": "proxiome-v2"
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},
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"pool1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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[
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"PIXELATOR_AMPLICON",
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"pixelator",
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"0.27.1"
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"0.27.2"
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]
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]
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}
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],
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"timestamp": "2026-05-27T13:29:11.737111296",
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"timestamp": "2026-05-29T14:05:38.535137938",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.5"
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"nextflow": "26.04.2"
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}
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},
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"PNA amplicon - small test": {
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[
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"PIXELATOR_AMPLICON",
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"pixelator",
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"0.27.1"
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"0.27.2"
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]
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]
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],

‎modules/local/pixelator/analysis/main.nf‎

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// conda "bioconda::pixelator=0.18.2"
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container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'quay.io/pixelgen-technologies/pixelator:0.27.1'
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: 'quay.io/pixelgen-technologies/pixelator:0.27.1'}"
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? 'quay.io/pixelgen-technologies/pixelator:0.27.2'
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: 'quay.io/pixelgen-technologies/pixelator:0.27.2'}"
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input:
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tuple val(meta), path(data)

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