Add Proxiome V2 workflow#204
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johandahlberg
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May 18, 2026
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johandahlberg
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Great work. I have looked over the code and run the test suite and everything looks good as far as I can tell.
| path(analysis_data , stageAs: "results/analysis/*"), | ||
| path(layout_data , stageAs: "results/layout/*") | ||
| ) | ||
| tuple val(meta), val(result_stages), path(results_data, arity: "1..*", stageAs: "results_raw/?/*") |
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This is a really nice change. Make this much easier to work with.
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| if (params.technology == "proxiome-v1" || params.technology == "nonhashed_samples") { | ||
| PIXELATOR_PNA_V1( | ||
| ch_reads, | ||
| ch_panel_files | ||
| ) | ||
| } else if (params.technology == "proxiome-v2" || params.technology == "hashed_samples") { | ||
| PIXELATOR_PNA_V2( | ||
| ch_reads, | ||
| ch_panel_files | ||
| ) | ||
| } else { | ||
| error "Unknown technology: \"${params.technology}\"" | ||
| } |
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Nice. I think this is clear.
This was referenced May 18, 2026
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This PR introduces the Proxiome V2 workflow to process pooled samples.
It also significantly reworks the tests:
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).Usage Documentation inWill be updated in a dedicated PRdocs/usage.mdis updated.Output Documentation inWill be updated in a dedicated PRdocs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).