Pass layout to the report stage

nf-core · May 27, 2024 · bd29d2c · bd29d2c
1 parent 1d2fcde
commit bd29d2c
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Showing 3 changed files with 10 additions and 1 deletion.
diff --git 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
@@ -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
@@ -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)