feat: unify summarised experiment

Author: atrigila

docs/output.md

@@ -728,15 +728,13 @@ 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.
+  - `<pseudo_aligner>.gene.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 transcript 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.
+  - `<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 abundance TPM (`tpm`), 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.
   </details>
 

modules.json

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