nf-core/pixelator: nf-core/pixelator 2.1.0

[2.1.0] - 2025-09-17

Enhancements & fixes

• Move to using quay.io as the container source, to avoid issues with users needing to login to access the Github Container Registry by @johandahlberg in #140
• Add a denoise step to the PNA workflow, that cleans data between the graph and analysis steps by @johandahlberg in #140
• Fix the PNA report not being generated by @fbdtemme in #142
• Template update for nf-core/tools v3.3.2 by @fbdtemme in #143
• Add the experiment_summary step which generates the Proximity Experiment Summary report by @johandahlberg in #144
• Switch PIXELATOR_PNA_LAYOUT process label to process_high to allocate less memory by @ptajvar in #147
• Simplify PNA_GENERATE_REPORTS subworkflow by @fbdtemme in #150

Parameters

| Old parameter | New parameter | | ------------- | -------------------------------------------- | | | --skip_denoise | | | --save_pna_denoise_pixelfile | | | --pna_denoise_run_one_core_graph_denoising | | | --pna_denoise_pval_threshold | | | --pna_denoise_inflate_factor | | | --pna_denoise_inflate_factor |

[!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.

Software dependencies

| Dependency | Old version | New version | | ------------- | ----------- | ----------- | | pixelator | 0.20.1 | 0.21.4 | | pixelatorES | | 0.4.3 |

[!NOTE] Dependency has been updated if both old and new parameter information is present. Dependency has been added if just the new parameter information is present. Dependency has been removed if new parameter information isn't present.