Simplify PNA_GENERATE_REPORTS subworkflow

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## [[2.1.0](https://github.com/nf-core/pixelator/releases/tag/x.x.x)] - YYYY-MM-DD
+## [[2.1.0](https://github.com/nf-core/pixelator/releases/tag/2.1.0)] - 2025-09-17
 
 ### Enhancements & fixes
 
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Template update for nf-core/tools v3.3.2 by @fbdtemme in [#143](https://github.com/nf-core/pixelator/pull/143)
 - Add the `experiment_summary` step which generates the Proximity Experiment Summary report by @johandahlberg in [#144](https://github.com/nf-core/pixelator/pull/144)
 - Switch PIXELATOR_PNA_LAYOUT process label to process_high to allocate less memory by @ptajvar in [#147](https://github.com/nf-core/pixelator/pull/147)
+- Simplify PNA_GENERATE_REPORTS subworkflow by @fbdtemme in [#150](https://github.com/nf-core/pixelator/pull/50)
 
 ### Parameters
 

modules/local/experiment_summary/main.nf

@@ -1,21 +1,23 @@
 process EXPERIMENT_SUMMARY {
     tag "${meta.id}"
     label "process_medium"
+
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelatores:0.4.3'
         : 'quay.io/pixelgen-technologies/pixelatores:0.4.3'}"
 
     input:
-    val(meta)
     path samplesheet_path
-    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 denoise_data                     , stageAs: "results/denoise/*"
-    path analysis_data                    , stageAs: "results/analysis/*"
-    path layout_data                      , stageAs: "results/layout/*"
-
+    tuple (
+        val(meta),
+        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(denoise_data  , stageAs: "results/denoise/*"),
+        path(analysis_data , stageAs: "results/analysis/*"),
+        path(layout_data   , stageAs: "results/layout/*")
+    )
 
     output:
     tuple val(meta), path("*experiment-summary.html")  , emit: html

modules/local/pixelator/single-cell-pna/report/main.nf

@@ -10,13 +10,18 @@ process PIXELATOR_PNA_REPORT {
         : 'quay.io/pixelgen-technologies/pixelator:0.21.4'}"
 
     input:
-    tuple val(meta), path(panel_file), val(panel)
-    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 layout_data,        stageAs: "results/layout/*"
+    tuple (
+        val(meta),
+        path(panel_file),
+        val(panel),
+        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(denoise_data, stageAs: "results/denoise/*"),
+        path(analysis_data, stageAs: "results/analysis/*"),
+        path(layout_data, stageAs: "results/layout/*")
+    )
 
     output:
     tuple val(meta), path("report/*.html"),    emit: report

modules/local/pixelator/single-cell-pna/report/tests/main.nf.test

@@ -16,31 +16,35 @@ nextflow_process {
                     [ id:'PNA055_Sample07_filtered_S7', design:'pna-2', panel:'proxiome-immuno-155', technology:'pna' ],
                     [],
                     'proxiome-immuno-155',
-                ]
-                input[1] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
-                ]
-                input[2] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
-                ]
-                input[3] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
-                ]
-                input[4] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true),
-                ]
-                input[5] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
-                ]
-                input[6] = [
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
-                    file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.graph.pxl', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ],
+                    [
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
+                    ]
                 ]
                 """
             }

modules/local/pixelator/single-cell-pna/report/tests/main.nf.test.snap

@@ -9,6 +9,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-28T06:27:29.902626458"
+        "timestamp": "2025-09-17T14:22:24.534737422"
     }
 }

subworkflows/local/pna/generate_reports.nf

@@ -42,81 +42,58 @@ workflow PNA_GENERATE_REPORTS {
             return [id, data]
         }
 
-    ch_panel_col = panel_files.map { meta, data -> [meta.id, data] }
-
-    ch_amplicon_col         = amplicon_data.map { meta, data -> [ meta.id, data] }
-    ch_demux_col            = demux_data.map { meta, data -> [ meta.id, data] }
-    ch_collapse_col         = collapse_data.map { meta, data -> [ meta.id, data] }
-    ch_graph_col            = graph_data.map { meta, data -> [meta.id, data] }
-    ch_analysis_col         = analysis_data.map { meta, data -> [meta.id, data] }
-    ch_denoise_col          = denoise_data.map { meta, data -> [meta.id, data] }
-    ch_layout_col           = layout_data.map { meta, data -> [meta.id, data] }
-
     ch_report_data = ch_meta_col
-        .concat ( ch_panel_col )
-        .concat ( ch_amplicon_col )
-        .concat ( ch_demux_col )
-        .concat ( ch_collapse_col )
-        .concat ( ch_graph_col )
-        .concat ( ch_denoise_col)
-        .concat ( ch_analysis_col )
-        .concat ( ch_layout_col )
-        .groupTuple (size: 9)
-
-    ch_split_report_data = ch_report_data.multiMap {
-        _id, data ->
-            panel_files:    [ data[0], data[1], data[1] ? null : data[0].panel ]
-            amplicon:       data[2] ? data[2].flatten() : []
-            demux:          data[3] ? data[3].flatten() : []
-            collapse:       data[4] ? data[4].flatten() : []
-            graph:          data[5] ? data[5].flatten() : []
-            denoise:        data[6] ? data[6].flatten() : []
-            analysis:       data[7] ? data[7].flatten() : []
-            layout:         data[8] ? data[8].flatten() : []
-    }
+        .join( panel_files.map   { meta, data -> [ meta.id, data ] } )
+        .join( amplicon_data.map { meta, data -> [ meta.id, data ] } )
+        .join( demux_data.map    { meta, data -> [ meta.id, data ] } )
+        .join( collapse_data.map { meta, data -> [ meta.id, data ] } )
+        .join( graph_data.map    { meta, data -> [ meta.id, data ] } )
+        .join( denoise_data.map  { meta, data -> [ meta.id, data ] } )
+        .join( analysis_data.map { meta, data -> [ meta.id, data ] } )
+        .join( layout_data.map   { meta, data -> [ meta.id, data ] } )
+
+    ch_pna_report_input = ch_report_data.map {
+        _id, meta, panels, amplicon, demux, collapse, graph, denoise, analysis, layout ->
+            [meta, panels, panels ? null : meta.panel, amplicon, demux, collapse, graph, denoise, analysis, layout]
+        }
 
-    PIXELATOR_PNA_REPORT (
-        ch_split_report_data.panel_files,
-        ch_split_report_data.amplicon,
-        ch_split_report_data.demux,
-        ch_split_report_data.collapse,
-        ch_split_report_data.graph,
-        ch_split_report_data.analysis,
-        ch_split_report_data.layout
-    )
-
-    ch_meta_grouped         = ch_report_data.map { _id, data -> data[0] }.flatten().collect().map {
-        def newMeta = [:]
-        newMeta.id = "all-samples"
-        newMeta.samples = it.collect { e -> e.id }
-        return newMeta
+    PIXELATOR_PNA_REPORT ( ch_pna_report_input )
+
+    // Accumulate results across all samples grouped per stage
+
+    def accumulator = [
+        meta: [ id: "all-samples", samples: [] ],
+        amplicon: [],
+        demux:    [],
+        collapse: [],
+        graph:    [],
+        denoise:  [],
+        analysis: [],
+        layout:   []
+    ]
+
+    ch_grouped_data = ch_report_data.reduce ( accumulator ) { acc, val ->
+        def (_id, meta, _panels, amplicon, demux, collapse, graph, denoise, analysis, layout) = val
+        acc.meta.samples += meta.id
+        acc.amplicon += amplicon
+        acc.demux    += demux
+        acc.collapse += collapse
+        acc.graph    += graph
+        acc.denoise  += denoise
+        acc.analysis += analysis
+        acc.layout   += layout
+        return acc
+    }.map { acc ->
+        [ acc.meta, acc.amplicon, acc.demux, acc.collapse, acc.graph, acc.denoise, acc.analysis, acc.layout ]
     }
 
-    ch_amplicon_flat        = ch_split_report_data.amplicon.flatten().collect()
-    ch_demux_flat           = ch_split_report_data.demux.flatten().collect()
-    ch_collapse_flat        = ch_split_report_data.collapse.flatten().collect()
-    ch_graph_flat           = ch_split_report_data.graph.flatten().collect()
-    ch_denoise_flat         = ch_split_report_data.denoise.flatten().collect()
-    ch_analysis_flat        = ch_split_report_data.analysis.flatten().collect()
-    ch_layout_flat          = ch_split_report_data.layout.flatten().collect()
-
-
     if (!skip_experiment_summary) {
-        EXPERIMENT_SUMMARY(
-            ch_meta_grouped,
-            samplesheet,
-            ch_amplicon_flat,
-            ch_demux_flat,
-            ch_collapse_flat,
-            ch_graph_flat,
-            ch_denoise_flat,
-            ch_analysis_flat,
-            ch_layout_flat
-        )
+        EXPERIMENT_SUMMARY ( samplesheet, ch_grouped_data )
+
         ch_versions           = ch_versions.mix(EXPERIMENT_SUMMARY.out.versions)
         ch_experiment_summary = EXPERIMENT_SUMMARY.out.html
     } else {
-        ch_experiment_summary = ch_meta_grouped.combine(Channel.of([]))
+        ch_experiment_summary = ch_grouped_data.map { it -> it[0] }.combine(Channel.of([]))
     }
 
     ch_versions = ch_versions.mix(PIXELATOR_PNA_REPORT.out.versions.first())