Release 3.0.0

.nf-core.yml

@@ -9,11 +9,11 @@ lint:
     - assets/nf-core-pixelator_logo_light.png
     - .github/PULL_REQUEST_TEMPLATE.md
   multiqc_config: false
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Pixelgen Technologies AB
-  description: Pipeline for analysis of Molecular Pixelation assays
+  description: Pipeline for analysis of Proximity Network Assay data
   force: false
   is_nfcore: true
   name: pixelator
@@ -23,4 +23,4 @@ template:
     - fastqc
     - multiqc
     - igenomes
-  version: 2.3.1
+  version: 3.0.0

CHANGELOG.md

@@ -3,7 +3,83 @@
 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).
 
-## [[2.3.1](https://github.com/nf-core/pixelator/releases/tag/2.3.1)] - 2025-01-14
+## [[3.0.0](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-02-23
+
+### Changed
+
+- Set default pna_graph_component_size_min_threshold to 8000 instead of null (i.e. automatic) by @ptajvar [#183](https://github.com/nf-core/pixelator/pull/183).
+
+### Removed
+
+- Support for MPX in the pipeline by @johandahlberg [#182](https://github.com/nf-core/pixelator/pull/182)
+
+### Enhancements & fixes
+
+- Update schema files (e.g. explicitly use integer types for integers, rather than numbers) by @johandahlberg [#184](https://github.com/nf-core/pixelator/pull/184), [#186](https://github.com/nf-core/pixelator/pull/186)
+- Add option to select custom containers for the experiment summary by @Aratz [#186](https://github.com/nf-core/pixelator/pull/186)
+
+### Parameters
+
+| Old parameter                            | New parameter                    |
+| ---------------------------------------- | -------------------------------- |
+|                                          | `--experiment_summary_container` |
+| `--save_amplicon_reads`                  |                                  |
+| `--trim_front`                           |                                  |
+| `--trim_tail`                            |                                  |
+| `--max_length`                           |                                  |
+| `--min_length`                           |                                  |
+| `--max_n_bases`                          |                                  |
+| `--avg_qual`                             |                                  |
+| `--dedup`                                |                                  |
+| `--remove_polyg`                         |                                  |
+| `--adapterqc_mismatches`                 |                                  |
+| `--save_qc_passed_reads`                 |                                  |
+| `--save_qc_failed_reads`                 |                                  |
+| `--demux_mismatches`                     |                                  |
+| `--demux_min_length`                     |                                  |
+| `--save_demux_processed_reads`           |                                  |
+| `--save_demux_failed_reads`              |                                  |
+| `--markers_ignore`                       |                                  |
+| `--algorithm`                            |                                  |
+| `--max_neighbours`                       |                                  |
+| `--collapse_mismatches`                  |                                  |
+| `--collapse_min_count`                   |                                  |
+| `--save_collapsed_reads`                 |                                  |
+| `--multiplet_recovery`                   |                                  |
+| `--graph_max_refinement_recursion_depth` |                                  |
+| `--graph_max_edges_to_split`             |                                  |
+| `--graph_min_count`                      |                                  |
+| `--save_edgelist`                        |                                  |
+| `--min_size`                             |                                  |
+| `--max_size`                             |                                  |
+| `--dynamic_filter`                       |                                  |
+| `--aggregate_calling`                    |                                  |
+| `--save_raw_component_metrics`           |                                  |
+| `--save_annotate_dataset`                |                                  |
+| `--skip_analysis`                        |                                  |
+| `--compute_polarization`                 |                                  |
+| `--compute_colocalization`               |                                  |
+| `--use_full_bipartite`                   |                                  |
+| `--polarization_transformation`          |                                  |
+| `--polarization_n_permutations`          |                                  |
+| `--polarization_min_marker_count`        |                                  |
+| `--colocalization_transformation`        |                                  |
+| `--colocalization_neighbourhood_size`    |                                  |
+| `--colocalization_n_permutations`        |                                  |
+| `--colocalization_min_region_count`      |                                  |
+| `--colocalization_min_marker_count`      |                                  |
+| `--save_analysis_dataset`                |                                  |
+| `--skip_layout`                          |                                  |
+| `--no_node_marker_counts`                |                                  |
+| `--layout_algorithm`                     |                                  |
+| `--skip_report`                          |                                  |
+
+> [!NOTE]
+> Parameter has been **updated** if both old and new parameter information is present.
+> Parameter has been **added** if just the new parameter information is present.
+> Parameter has been **removed** if new parameter information isn't present.
+
+## [[2.3.1](https://github.com/nf-core/pixelator/releases/tag/2.3.1)] - 2026-01-14
 
 - Update usage documentation by @vincent-van-hoef [#176](https://github.com/nf-core/pixelator/pull/176)
 - Use PNA data in test profile by @Aratz [#177](https://github.com/nf-core/pixelator/pull/177)

CITATIONS.md

@@ -12,7 +12,7 @@
 
 - [pixelator](https://doi.org/10.1038/s41592-024-02268-9)
 
-  > Karlsson, F., Kallas, T., Thiagarajan, D. et al. “Molecular pixelation: spatial proteomics of single cells by sequencing.“ Nat Methods 21, 1044–1052 (2024). https://doi.org/10.1038/s41592-024-02268-9
+  > Karlsson, F., Simonetti, M.,Galonska, C. et al. "Single-Cell Protein Interactomes by the Proximity Network Assay". _bioRxiv_ 2025.06.19.660329; doi: [10.1101/2025.06.19.660329](https://doi.org/10.1101/2025.06.19.660329)
 
 - [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)
 

README.md

@@ -13,7 +13,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -24,14 +24,12 @@
 ## Introduction
 
 **nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of data from the
-Molecular Pixelation (MPX) and Proximity Network (PNA) assays. It takes a samplesheet as input and will process your data
+Proximity Network (PNA) assay. It takes a samplesheet as input and will process your data
 using `pixelator` to produce a PXL file containing single-cell protein abundance and protein interactomics data.
 
 ![](./docs/images/nf-core-pixelator-metromap.svg)
 
-Depending on the input data the pipeline will run different steps.
-
-For PNA data, the pipeline will run the following steps:
+The pipeline will run the following steps:
 
 1. Do quality control checks of input reads and build amplicons ([`pixelator single-cell-pna amplicon`](https://github.com/PixelgenTechnologies/pixelator))
 2. Create groups of amplicons based on their marker assignments ([`pixelator single-cell-pna demux`](https://github.com/PixelgenTechnologies/pixelator))
@@ -42,17 +40,9 @@ For PNA data, the pipeline will run the following steps:
 7. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-pna layout`](https://github.com/PixelgenTechnologies/pixelator))
 8. Proxiome Experiment Summary generation using [PixelatorES](https://github.com/PixelgenTechnologies/pixelatorES)
 
-For MPX data, the pipeline will run the following steps:
-
-1. Build an amplicons from the input reads ([`pixelator single-cell-mpx amplicon`](https://github.com/PixelgenTechnologies/pixelator))
-2. Read QC and filtering, correctness of the pixel binding sequence sequences ([`pixelator single-cell-mpx preqc | pixelator adapterqc`](https://github.com/PixelgenTechnologies/pixelator))
-3. Assign a marker (barcode) to each read ([`pixelator single-cell-mpx demux`](https://github.com/PixelgenTechnologies/pixelator))
-4. Error correction, duplicate removal, compute read counts ([`pixelator single-cell-mpx collapse`](https://github.com/PixelgenTechnologies/pixelator))
-5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator single-cell-mpx graph`](https://github.com/PixelgenTechnologies/pixelator))
-6. Call and annotate cells ([`pixelator single-cell-mpx annotate`](https://github.com/PixelgenTechnologies/pixelator))
-7. Analyze the cells for polarization and colocalization ([`pixelator single-cell-mpx analysis`](https://github.com/PixelgenTechnologies/pixelator))
-8. Generate 3D graph layouts for visualization of cells ([`pixelator single-cell-mpx layout`](https://github.com/PixelgenTechnologies/pixelator))
-9. Report generation ([`pixelator single-cell-mpx report`](https://github.com/PixelgenTechnologies/pixelator))
+> [!NOTE]
+> If you are looking to run the pipeline with Molecular Pixelation (MPX) data. Please refer to the [release 2.3.1](https://nf-co.re/pixelator/2.3.1/),
+> which is the last version to support that data type.
 
 > [!WARNING]
 > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
@@ -128,13 +118,7 @@ You can cite the `nf-core` publication as follows:
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
 
-You can cite the molecular pixelation technology as follows:
-
-> **Molecular pixelation: spatial proteomics of single cells by sequencing.**
->
-> Filip Karlsson, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, Sylvain Geny, Erik Pettersson, Jan Rhomberg-Kauert, Ludvig Larsson, Hanna van Ooijen, Stefan Petkov, Marcela González-Granillo, Jessica Bunz, Johan Dahlberg, Michele Simonetti, Prajakta Sathe, Petter Brodin, Alvaro Martinez Barrio & Simon Fredriksson
->
-> _Nat Methods._ 2024 May 08. doi: [10.1038/s41592-024-02268-9](https://doi.org/10.1038/s41592-024-02268-9)
+You can cite the Proximity Network Technology as follows:
 
 > **Single-Cell Protein Interactomes by the Proximity Network Assay.**
 >

assets/email_template.html

@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/pixelator: Pipeline for analysis of Molecular Pixelation assays">
+  <meta name="description" content="nf-core/pixelator: Pipeline for analysis of Proximity Network Assay data">
   <title>nf-core/pixelator Pipeline Report</title>
 </head>
 <body>

assets/schema_input.json

@@ -7,45 +7,66 @@
     "items": {
         "type": "object",
         "required": ["sample", "design", "fastq_1"],
+        "additionalProperties": false,
         "properties": {
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "description": "Sample name (no spaces).",
                 "meta": ["id"]
             },
             "design": {
                 "type": "string",
-                "meta": ["design"],
-                "errorMessage": "Design must be specified"
+                "pattern": "^\\S+$",
+                "errorMessage": "Design must be specified",
+                "description": "Design identifier (no spaces).",
+                "meta": ["design"]
             },
             "panel": {
-                "errorMessage": "Panel name must be specified",
                 "type": "string",
+                "pattern": "^\\S+$",
+                "description": "Panel identifier (no spaces).",
+                "errorMessage": "panel or panel_file must be specified",
                 "meta": ["panel"]
             },
             "panel_file": {
+                "type": "string",
+                "description": "Optional panel file path. Empty string allowed. If set, must end with .csv, .tsv, .yaml, or .yml and contain no spaces.",
                 "errorMessage": "Panel file must either be left empty or cannot contain spaces and must have extension '.csv', '.tsv' or '.yaml'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+.(csv|tsv|ya?ml)$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
+                "pattern": "^$|^\\S+\\.(csv|tsv|ya?ml)$"
             },
             "fastq_1": {
                 "type": "string",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "description": "FASTQ(.gz) path for read 1 (no spaces).",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "description": "Optional FASTQ(.gz) path for read 2 (no spaces)."
+            },
+            "condition": {
+                "type": "string",
+                "description": "Optional experimental condition for the sample.",
+                "meta": ["condition"]
+            },
+            "reference_condition": {
+                "type": "string",
+                "description": "Optional reference condition for differential analysis.",
+                "meta": ["reference_condition"]
+            },
+            "sample_alias": {
+                "type": "string",
+                "description": "Optional alternative sample name.",
+                "meta": ["sample_alias"]
+            },
+            "alternative_condition": {
+                "type": "string",
+                "description": "Optional alternative condition for the sample.",
+                "meta": ["alternative_condition"]
             }
         }
     }