diff --git a/modules/local/pixelator/single-cell/report/main.nf b/modules/local/pixelator/single-cell/report/main.nf index 93e1b5d..6d891a6 100644 --- a/modules/local/pixelator/single-cell/report/main.nf +++ b/modules/local/pixelator/single-cell/report/main.nf @@ -18,6 +18,7 @@ process PIXELATOR_REPORT { path graph_data , stageAs: "results/graph/*" path annotate_data , stageAs: "results/annotate/*" path analysis_data , stageAs: "results/analysis/*" + path layout_data , stageAs: "results/layout/*" output: diff --git a/subworkflows/local/generate_reports.nf b/subworkflows/local/generate_reports.nf index dc5fb42..73c599b 100644 --- a/subworkflows/local/generate_reports.nf +++ b/subworkflows/local/generate_reports.nf @@ -24,6 +24,7 @@ workflow GENERATE_REPORTS { graph_data // channel: [meta, [path, ...]] annotate_data // channel: [meta, [path, ...]] analysis_data // channel: [meta, [path, ...]] + layout_data // channel: [meta, [path, ...]] main: ch_versions = Channel.empty() @@ -57,6 +58,7 @@ workflow GENERATE_REPORTS { ch_graph_col = graph_data.map { meta, data -> [meta.id, data] } ch_annotate_col = annotate_data.map { meta, data -> [meta.id, data] } ch_analysis_col = analysis_data.map { meta, data -> [meta.id, data] } + ch_layout_col = layout_data.map { meta, data -> [meta.id, data] } // // Combine all inputs and group them, then split them up again. @@ -87,6 +89,7 @@ workflow GENERATE_REPORTS { .concat ( ch_graph_col ) .concat ( ch_annotate_col ) .concat ( ch_analysis_col ) + .concat ( ch_layout_col ) .groupTuple (size: 10) // @@ -108,6 +111,7 @@ workflow GENERATE_REPORTS { ch_graph_grouped = ch_report_data.map { id, data -> data[7] ? data[7].flatten() : [] } ch_annotate_grouped = ch_report_data.map { id, data -> data[8] ? data[8].flatten() : [] } ch_analysis_grouped = ch_report_data.map { id, data -> data[9] ? data[9].flatten() : [] } + ch_layout_grouped = ch_report_data.map { id, data -> data[10] ? data[10].flatten() : [] } // // MODULE: Run pixelator single-cell report for each samples @@ -124,6 +128,7 @@ workflow GENERATE_REPORTS { ch_graph_grouped, ch_annotate_grouped, ch_analysis_grouped, + ch_layout_grouped, ) ch_versions = ch_versions.mix(PIXELATOR_REPORT.out.versions.first()) diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index 5091a14..ab03c7a 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -201,6 +201,7 @@ workflow PIXELATOR { // // MODULE: Run pixelator single-cell layout + // PIXELATOR_LAYOUT ( ch_analysed ) ch_layout = PIXELATOR_LAYOUT.out.dataset ch_versions = ch_versions.mix(PIXELATOR_LAYOUT.out.versions.first()) @@ -230,6 +231,7 @@ workflow PIXELATOR { ch_cluster_data = PIXELATOR_GRAPH.out.all_results ch_annotate_data = PIXELATOR_ANNOTATE.out.all_results ch_analysis_data = PIXELATOR_ANALYSIS.out.all_results + ch_layout_data = PIXELATOR_ANALYSIS.out.all_results GENERATE_REPORTS( ch_cat_panel_files, @@ -240,7 +242,8 @@ workflow PIXELATOR { ch_collapse_data, ch_cluster_data, ch_annotate_data, - ch_analysis_data + ch_analysis_data, + ch_layout_data ) ch_versions = ch_versions.mix(GENERATE_REPORTS.out.versions)