From f442540571a628df90ad1f08a9b1f315de19fa4c Mon Sep 17 00:00:00 2001
From: d4straub <daniel.straub@uni-tuebingen.de>
Date: Fri, 20 Dec 2024 15:25:07 +0100
Subject: [PATCH] add TreeSE to report

---
 assets/report_template.Rmd      | 33 ++++++++++++++++++++++++++-------
 modules/local/summary_report.nf |  2 ++
 workflows/ampliseq.nf           |  4 ++--
 3 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd
index 76119739..50d077b0 100644
--- a/assets/report_template.Rmd
+++ b/assets/report_template.Rmd
@@ -107,6 +107,7 @@ params:
     picrust_pathways: FALSE
     sbdi: FALSE
     phyloseq: FALSE
+    tse: FALSE
 ---
 
 <!-- Load libraries -->
@@ -1615,19 +1616,37 @@ but if you run nf-core/ampliseq with a sample metadata table (`--metadata`) any
 "))
 ```
 
-<!-- Section on PHYLOSEQ results -->
+<!-- Section on exported R objects -->
 
-```{r, eval = !isFALSE(params$phyloseq), results='asis'}
+```{r, results='asis'}
+any_robject <- !isFALSE(params$phyloseq) || !isFALSE(params$tse)
+```
+
+```{r, eval = !isFALSE(params$any_robject), results='asis'}
 cat(paste0("
-# Phyloseq
+# R objects
 
-[Phyloseq](https://doi.org/10.1371/journal.pone.0061217)
-is a popular R package to analyse and visualize microbiom data.
-The produced RDS files contain phyloseq objects and can be loaded directely into R and phyloseq.
+Microbiome data can be analysed and visualized with certain R packages. For convenience, R objects in RDS format are provided.
+"))
+
+if ( !isFALSE(params$phyloseq) ) {
+    cat(paste0("
+[Phyloseq](https://doi.org/10.1371/journal.pone.0061217) objects and can be loaded directely into R with package 'phyloseq'.
 The objects contain an ASV abundance table and a taxonomy table.
 If available, metadata and phylogenetic tree will also be included in the phyloseq object.
 The files can be found in folder [phyloseq](../phyloseq/).
-"))
+    "))
+}
+
+if ( !isFALSE(params$tse) ) {
+    cat(paste0("
+[TreeSummarizedExperiment](https://doi.org/10.12688/f1000research.26669.2) (TreeSE, TSE)
+objects can be loaded into R with package 'TreeSummarizedExperiment'. and contain an ASV abundance table,
+a taxonomy table, and sequences.
+If available, metadata and phylogenetic tree will also be included in the object.
+The files can be found in folder [treesummarizedexperiment](../treesummarizedexperiment/).
+    "))
+}
 ```
 
 <!-- Section on methods -->
diff --git a/modules/local/summary_report.nf b/modules/local/summary_report.nf
index 309dcdf7..61c93733 100644
--- a/modules/local/summary_report.nf
+++ b/modules/local/summary_report.nf
@@ -58,6 +58,7 @@ process SUMMARY_REPORT  {
     path(picrust_pathways)
     path(sbdi, stageAs: 'sbdi/*')
     path(phyloseq, stageAs: 'phyloseq/*')
+    path(tse, stageAs: 'tse/*')
 
     output:
     path "*.svg"               , emit: svg, optional: true
@@ -137,6 +138,7 @@ process SUMMARY_REPORT  {
         ancombc_formula ? "ancombc_formula='"+ ancombc_formula.join(",") +"'" : "",
         sbdi ? "sbdi='"+ sbdi.join(",") +"'" : "",
         phyloseq ? "phyloseq='"+ phyloseq.join(",") +"'" : "",
+        tse ? "tse='"+ tse.join(",") +"'" : "",
     ]
     // groovy list to R named list string; findAll removes empty entries
     params_list_named_string = params_list_named.findAll().join(',').trim()
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index 10a34b0c..e7014263 100644
--- a/workflows/ampliseq.nf
+++ b/workflows/ampliseq.nf
@@ -1016,8 +1016,8 @@ workflow AMPLISEQ {
             run_qiime2 && params.ancombc_formula && params.metadata ? QIIME2_ANCOM.out.ancombc_formula.collect().ifEmpty( [] ) : [],
             params.picrust ? PICRUST.out.pathways.ifEmpty( [] ) : [],
             params.sbdiexport ? SBDIEXPORT.out.sbditables.mix(SBDIEXPORTREANNOTATE.out.sbdiannottables).collect().ifEmpty( [] ) : [],
-            !params.skip_taxonomy && !params.skip_phyloseq ? ROBJECT_WORKFLOW.out.phyloseq.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : []
-            //TODO: add treesummarizedexperiment
+            !params.skip_taxonomy && !params.skip_phyloseq ? ROBJECT_WORKFLOW.out.phyloseq.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : [],
+            !params.skip_taxonomy && !params.skip_tse ? ROBJECT_WORKFLOW.out.tse.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : []
         )
         ch_versions    = ch_versions.mix(SUMMARY_REPORT.out.versions)
     }