Merge pull request #1550 from atrigila/unify_summarised_experiment

Unify summarised experiment

Author: atrigila

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1528](https://github.com/nf-core/rnaseq/pull/1528) - Improve JSON schema validation files
 - [PR #1523](https://github.com/nf-core/rnaseq/pull/1523) - Update preprocessing subworkflow to fix linting block on trimming
 - [PR #1521](https://github.com/nf-core/rnaseq/pull/1521) - Updated Perl conda package version for local module gtf2bed for Arm compatibility.
+- [PR #1550](https://github.com/nf-core/rnaseq/pull/1550) - Simplify `SummarizedExperiment` outputs.
 - [PR #1553](https://github.com/nf-core/rnaseq/pull/1553) - Make jobs automatically resubmit for exit code 175
 
 # 3.18.0 - 2024-12-19

docs/output.md

@@ -728,16 +728,33 @@ The principal output files are the same between Salmon and Kallisto:
 - `<pseudo_aligner>/`
   - `<pseudo_aligner>.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
   - `<pseudo_aligner>.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
-  - `<pseudo_aligner>.gene_counts.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated counts (`counts`) and transcript length (`length`) in the assays slot for genes.
+  - `all_samples_gene.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated counts (`counts`) and gene length (`length`), estimated library size-scaled counts (`counts_scaled`), estimated length-scaled counts (`counts_length_scaled`) in the assays slot for genes.
   - `<pseudo_aligner>.merged.gene_lengths.tsv`: Matrix of average within-sample transcript lengths for each gene across all samples.
   - `<pseudo_aligner>.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled estimated counts across all samples.
-  - `<pseudo_aligner>.merged.gene_counts_scaled.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated library size-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
   - `<pseudo_aligner>.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
-  - `<pseudo_aligner>.merged.gene_counts_length_scaled.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated length-scaled counts (`counts`) and transcript length (`length`) in the assays slot for genes.
   - `<pseudo_aligner>.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
   - `<pseudo_aligner>.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
-  - `<pseudo_aligner>.merged.transcript_counts.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the TPM (`abundance`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
   - `tx2gene.tsv`: Tab-delimited file containing gene to transcripts ids mappings.
+  - `all_samples_transcript.SummarizedExperiment.rds`: RDS object that can be loaded in R that contains a [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) container with the abundance TPM (`tpm`), estimated isoform-level raw counts (`counts`) and transcript length (`length`) in the assays slot for transcripts.
+
+> **TIP:** You can access specific assay matrices from the `SummarizedExperiment` RDS object with the following R code:
+
+```r
+  library(SummarizedExperiment)
+
+  # Load the RDS object
+  se <- readRDS("all_samples_gene.SummarizedExperiment.rds")
+
+  # View available assays
+  assayNames(se)
+
+  # Access a specific assay, e.g., length-scaled counts
+  counts_length_scaled <- assay(se, "counts_length_scaled")
+
+  # Print the matrix
+  print(counts_length_scaled)
+```
+
   </details>
 
 An additional subset of files are distinct to each tool, for Salmon:

modules.json

@@ -373,7 +373,7 @@
                     },
                     "quantify_pseudo_alignment": {
                         "branch": "master",
-                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "git_sha": "1f008221e451e7a4738226c49e69aaa2eb731369",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {