Merge pull request #619 from d4straub/add_phyloseq_output

add SBDI export and phyloseq output to summary report

CHANGELOG.md

@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#558](https://github.com/nf-core/ampliseq/pull/558) - Pipeline summary report
+- [#558](https://github.com/nf-core/ampliseq/pull/558),[#619](https://github.com/nf-core/ampliseq/pull/619) - Pipeline summary report
+- [#615](https://github.com/nf-core/ampliseq/pull/615) - Phyloseq R object creation
 
 ### `Changed`
 

README.md

@@ -88,6 +88,7 @@ nf-core/ampliseq was originally written by Daniel Straub ([@d4straub](https://gi
 
 We thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order):
 
+- [Adam Bennett](https://github.com/a4000)
 - [Diego Brambilla](https://github.com/DiegoBrambilla)
 - [Emelie Nilsson](https://github.com/emnilsson)
 - [Jeanette Tångrot](https://github.com/jtangrot)

assets/report_template.Rmd

@@ -95,6 +95,8 @@ params:
     diversity_indices_beta: FALSE
     diversity_indices_adonis: ""
     picrust_pathways: FALSE
+    sbdi: FALSE
+    phyloseq: FALSE
 ---
 
 <!-- Load libraries -->
@@ -1379,11 +1381,11 @@ for (folder in ancom) {
 }
 ```
 
-<!-- Subsection on PICRUSt2 results -->
+<!-- Section on PICRUSt2 results -->
 
 ```{r, eval = !isFALSE(params$picrust_pathways), results='asis'}
 cat(paste0("
-## PICRUSt2
+# PICRUSt2
 
 [PICRUSt2](https://pubmed.ncbi.nlm.nih.gov/32483366/) (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)
 is a software for predicting functional abundances based only on marker gene sequences.
@@ -1394,6 +1396,37 @@ see `METACYC_path_abun_unstrat_descrip.tsv`. Quantifications are not normalized
 "))
 ```
 
+<!-- Section on SBDI results -->
+
+```{r, eval = !isFALSE(params$sbdi), results='asis'}
+cat(paste0("
+# SBDI
+
+The [Swedish Biodiversity Infrastructure (SBDI)](https://biodiversitydata.se/) provides a cost-effective, cutting-edge
+infrastructure that supports Swedish and international biodiversity and ecosystems research.
+Files in preparation for submission to SBDI can be found in folder [SBDI](../SBDI/).
+Tables are generated from the DADA2 denoising and taxonomy assignment steps.
+Each table, except `annotation.tsv`, corresponds to one tab in the [SBDI submission template](https://asv-portal.biodiversitydata.se/submit).
+Most of the fields in the template will not be populated,
+but if you run nf-core/ampliseq with a sample metadata table (`--metadata`) any fields corresponding to a field in the template will be used.
+"))
+```
+
+<!-- Section on PHYLOSEQ results -->
+
+```{r, eval = !isFALSE(params$phyloseq), results='asis'}
+cat(paste0("
+# Phyloseq
+
+[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.
+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/).
+"))
+```
+
 <!-- Section on methods -->
 
 # Methods

modules/local/summary_report.nf

@@ -50,7 +50,8 @@ process SUMMARY_REPORT  {
     path(diversity_indices_adonis, stageAs: 'beta_diversity/adonis/*') // prevent folder name collisons
     path(ancom)
     path(picrust_pathways)
-
+    path(sbdi, stageAs: 'sbdi/*')
+    path(phyloseq, stageAs: 'phyloseq/*')
 
     output:
     path "*.svg"               , emit: svg, optional: true
@@ -119,6 +120,8 @@ process SUMMARY_REPORT  {
         diversity_indices ? "diversity_indices_depth='$diversity_indices',diversity_indices_beta='"+ diversity_indices_beta.join(",") +"'" : "",
         diversity_indices_adonis ? "diversity_indices_adonis='"+ diversity_indices_adonis.join(",") +"',qiime_adonis_formula='$params.qiime_adonis_formula'" : "",
         ancom ? "ancom='"+ ancom.join(",") +"'" : "",
+        sbdi ? "sbdi='"+ sbdi.join(",") +"'" : "",
+        phyloseq ? "phyloseq='"+ phyloseq.join(",") +"'" : "",
     ]
     // groovy list to R named list string; findAll removes empty entries
     params_list_named_string = params_list_named.findAll().join(',').trim()

workflows/ampliseq.nf

@@ -798,7 +798,9 @@ workflow AMPLISEQ {
             run_qiime2 && !params.skip_diversity_indices && params.metadata ? QIIME2_DIVERSITY.out.beta.collect().ifEmpty( [] ) : [],
             run_qiime2 && !params.skip_diversity_indices && params.metadata ? QIIME2_DIVERSITY.out.adonis.collect().ifEmpty( [] ) : [],
             run_qiime2 && !params.skip_ancom && params.metadata ? QIIME2_ANCOM.out.ancom.collect().ifEmpty( [] ) : [],
-            params.picrust ? PICRUST.out.pathways.ifEmpty( [] ) : []
+            params.picrust ? PICRUST.out.pathways.ifEmpty( [] ) : [],
+            params.sbdiexport ? SBDIEXPORT.out.sbditables.mix(SBDIEXPORTREANNOTATE.out.sbdiannottables).collect().ifEmpty( [] ) : [],
+            !params.skip_taxonomy ? PHYLOSEQ_WORKFLOW.out.rds.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : []
         )
         ch_versions    = ch_versions.mix(SUMMARY_REPORT.out.versions)
     }