Merge pull request #1592 from nf-core/prep_release

Bump version to 3.20.0 ahead of release

Author: pinin4fjords

.nf-core.yml

@@ -14,11 +14,11 @@ nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: "Harshil Patel, Phil Ewels, Rickard Hammarén"
-  description: RNA sequencing analysis pipeline for gene/isoform quantification and
-    extensive quality control.
+  description: RNA sequencing analysis pipeline for gene/isoform quantification
+    and extensive quality control.
   force: false
   is_nfcore: true
   name: rnaseq
   org: nf-core
   outdir: .
-  version: 3.20.0dev
+  version: 3.20.0

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 3.20.0dev
+## 3.20.0
 
 ### Credits
 

docs/output.md

@@ -215,6 +215,21 @@ When `--remove_ribo_rna` is specified, the pipeline uses [SortMeRNA](https://git
 - `star_salmon/`
   - `*.Aligned.out.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the reference genome will be placed in this directory.
   - `*.Aligned.toTranscriptome.out.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the transcriptome will be placed in this directory.
+  - `salmon.merged.gene_counts.tsv`: Matrix of gene-level raw counts across all samples.
+  - `salmon.merged.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
+  - `salmon.merged.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.
+  - `salmon.merged.gene_lengths.tsv`: Matrix of average within-sample transcript lengths for each gene across all samples.
+  - `salmon.merged.gene_counts_scaled.tsv`: Matrix of gene-level library size-scaled estimated counts across all samples.
+  - `salmon.merged.gene_counts_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
+  - `salmon.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
+  - `salmon.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
+  - `tx2gene.tsv`: Tab-delimited file containing gene to transcripts ids mappings.
+  - `salmon.merged.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.
+- `star_salmon/<SAMPLE>/`
+  - `quant.sf`: Salmon transcript-level quantification results.
+  - `quant.genes.sf`: Salmon gene-level quantification results.
+- `star_salmon/<SAMPLE>/logs/`
+  - `salmon_quant.log`: Salmon quantification log file.
 - `star_salmon/log/`
   - `*.SJ.out.tab`: File containing filtered splice junctions detected after mapping the reads.
   - `*.Log.final.out`: STAR alignment report containing the mapping results summary.
@@ -224,6 +239,23 @@ When `--remove_ribo_rna` is specified, the pipeline uses [SortMeRNA](https://git
 
 </details>
 
+:::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("salmon.merged.gene.SummarizedExperiment.rds")
+
+  # View available assays
+  assayNames(se)
+
+  # Access a specific assay, e.g., length-scaled counts
+  assay(se, "counts_length_scaled")
+```
+
 [STAR](https://github.com/alexdobin/STAR) is a read aligner designed for splice aware mapping typical of RNA sequencing data. STAR stands for *S*pliced *T*ranscripts *A*lignment to a *R*eference, and has been shown to have high accuracy and outperforms other aligners by more than a factor of 50 in mapping speed, but it is memory intensive. Using `--aligner star_salmon` is the default alignment and quantification option.
 
 The STAR section of the MultiQC report shows a bar plot with alignment rates: good samples should have most reads as _Uniquely mapped_ and few _Unmapped_ reads.
@@ -728,14 +760,14 @@ 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.
-  - `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.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_length_scaled.tsv`: Matrix of gene-level length-scaled estimated counts across all samples.
   - `<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.
   - `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.
+  - `<pseudo_aligner>.merged.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:
@@ -745,7 +777,7 @@ You can access specific assay matrices from the `SummarizedExperiment` RDS objec
   library(SummarizedExperiment)
 
   # Load the RDS object
-  se <- readRDS("all_samples_gene.SummarizedExperiment.rds")
+  se <- readRDS("salmon.merged.gene.SummarizedExperiment.rds")  # or kallisto.merged.gene.SummarizedExperiment.rds
 
   # View available assays
   assayNames(se)

nextflow.config

@@ -413,7 +413,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.10.5'
-    version         = '3.20.0dev'
+    version         = '3.20.0'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }