From c7a322dc7ac593cf2e15714d712554930ffcc266 Mon Sep 17 00:00:00 2001 From: d4straub Date: Fri, 20 Dec 2024 14:44:50 +0100 Subject: [PATCH] update docs --- CHANGELOG.md | 1 + docs/output.md | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 332a6b45..d21ec79b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#798](https://github.com/nf-core/ampliseq/pull/798) - Added SILVA version 138.2 of DADA2 taxonomy database: `silva=138.2` or `silva` as parameter to `--dada2_ref_taxonomy` - [#804](https://github.com/nf-core/ampliseq/pull/804) - Added version 10 of Unite as parameter for `--dada_ref_taxonomy` (issue [#768](https://github.com/nf-core/ampliseq/issues/768)) +- [#807](https://github.com/nf-core/ampliseq/pull/807) - Export of TreeSummarizedExperiment R object by default, can be omitted with `--skip_tse`, also added ability to skip phyloseq R object generation with `--skip_phyloseq` ### `Changed` diff --git a/docs/output.md b/docs/output.md index 33278748..387d5dc3 100644 --- a/docs/output.md +++ b/docs/output.md @@ -46,7 +46,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Differential abundance analysis](#differential-abundance-analysis) - Calling differentially abundant features with ANCOM or ANCOM-BC - [PICRUSt2](#picrust2) - Predict the functional potential of a bacterial community - [SBDI export](#sbdi-export) - Swedish Biodiversity Infrastructure (SBDI) submission file -- [Phyloseq](#phyloseq) - Phyloseq R objects +- [R object](#r-objects) - Phyloseq and TreeSummarizedExperiment R objects - [Read count report](#read-count-report) - Report of read counts during various steps of the pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution @@ -629,15 +629,17 @@ Most of the fields in the template will not be populated by the export process, -### Phyloseq +### R objects -This directory will hold phyloseq objects for each taxonomy table produced by this pipeline. The objects will contain an ASV abundance table and a taxonomy table. If the pipeline is provided with metadata, that metadata will also be included in the phyloseq object. A phylogenetic tree will also be included if the pipeline produces a tree. +Pipeline results are stored in phyloseq and TreeSummarizedExperiment R objects for each taxonomy table produced by this pipeline. The R objects will contain an ASV abundance table and a taxonomy table, and optionally sequences, metadata and a phylogenetic tree.
Output files - `phyloseq/` - `_phyloseq.rds`: Phyloseq R object. +- `treesummarizedexperiment/` + - `_TreeSummarizedExperiment.rds`: TreeSummarizedExperiment R object.