Update to pixelator 0.20.x #131
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.1.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
johandahlberg
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fbdtemme
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May 16, 2025
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| path "design_options.txt", emit: designs | ||
| path "panel_options.txt", emit: panels | ||
| path "versions.yml", emit: versions |
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| tuple val(meta), path("amplicon/*.report.json"), emit: report_json | ||
| tuple val(meta), path("amplicon/*.meta.json"), emit: metadata | ||
| tuple val(meta), path("*pixelator-amplicon.log"), emit: log |
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| tuple val(meta), path("analysis/*dataset.pxl"), emit: dataset | ||
| tuple val(meta), path("analysis/*report.json"), emit: report_json | ||
| tuple val(meta), path("analysis/*.meta.json"), emit: metadata | ||
| tuple val(meta), path("analysis/*"), emit: all_results | ||
| tuple val(meta), path("*pixelator-analysis.log"), emit: log | ||
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| path "versions.yml" , emit: versions | ||
| path "versions.yml", emit: versions | ||
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| tuple val(meta), path("annotate/*.dataset.pxl"), emit: dataset | ||
| tuple val(meta), path("annotate/*.report.json"), emit: report_json | ||
| tuple val(meta), path("annotate/*.meta.json"), emit: metadata | ||
| tuple val(meta), path("annotate/*"), emit: all_results | ||
| tuple val(meta), path("*pixelator-annotate.log"), emit: log | ||
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| path "versions.yml" , emit: versions | ||
| path "versions.yml", emit: versions |
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| tuple val(meta), path("collapse/*.report.json"), emit: report_json | ||
| tuple val(meta), path("collapse/*.meta.json"), emit: metadata | ||
| tuple val(meta), path("*pixelator-collapse.log"), emit: log | ||
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| path "versions.yml" , emit: versions | ||
| path "versions.yml", emit: versions |
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| path amplicon_data, stageAs: "results/amplicon/*" | ||
| path preqc_data, stageAs: "results/preqc/*" | ||
| path adapterqc_data, stageAs: "results/adapterqc/*" | ||
| path demux_data, stageAs: "results/demux/*" | ||
| path collapse_data, stageAs: "results/collapse/*" | ||
| path graph_data, stageAs: "results/graph/*" | ||
| path annotate_data, stageAs: "results/annotate/*" | ||
| path analysis_data, stageAs: "results/analysis/*" | ||
| path layout_data, stageAs: "results/layout/*" |
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| tuple val(meta), path("report/*.html"), emit: reports | ||
| tuple val(meta), path("*pixelator-*.log"), emit: log | ||
| path "versions.yml", emit: versions |
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| path amplicon_data, stageAs: "results/amplicon/*" | ||
| path demux_data, stageAs: "results/demux/*" | ||
| path collapse_data, stageAs: "results/collapse/*" | ||
| path graph_data, stageAs: "results/graph/*" | ||
| path analysis_data, stageAs: "results/analysis/*" | ||
| path post_analysis_data, stageAs: "results/post_analysis/*" | ||
| path layout_data, stageAs: "results/layout/*" |
| @@ -129,12 +128,12 @@ workflow GENERATE_REPORTS { | |||
| ch_report_inputs.graph, | |||
| ch_report_inputs.annotate, | |||
| ch_report_inputs.analysis, | |||
| ch_report_inputs.layout | |||
| ch_report_inputs.layout, | |||
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Does the trailing comma's here work? I thought it wasn't allowed.
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I think so. But I will remove it just to be sure.
subworkflows/local/pna/main.nf
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| workflow PNA { | ||
| take: | ||
| fastq // channel: [ meta, [path(sample_1.fq), path(sample_2.fq)] ] | ||
| panel_files // channel [ meta, path(panel_file) | ] |
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Suggested change
| panel_files // channel [ meta, path(panel_file) | ] | |
| panel_files // channel: [ meta, path(panel_file) | ] |
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This is PR brings the changes to the pipeline to support the Proximity Network Assay (PNA) from Pixelgen Technologies. It splits the pipeline into two subworkflows, the existing one for MPX and a new one for PNA.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).