Fix #762 and #775

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).
 
-## [[3.7](https://github.com/nf-core/rnaseq/releases/tag/3.7)] - 2022-04-29
+## [[3.7](https://github.com/nf-core/rnaseq/releases/tag/3.7)] - 2022-05-03
 
 ### :warning: Major enhancements
 
@@ -12,7 +12,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#762](https://github.com/nf-core/rnaseq/issues/762)] - Explicitly set `--skip_bbsplit false` with `--bbsplit_fasta_list` to use BBSplit
 - [[#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
+- [[#775](https://github.com/nf-core/rnaseq/issues/775)] - Incorrect columns in Salmon transcript files
 - [[#791](https://github.com/nf-core/rnaseq/issues/791)] - Add outputs for umitools dedup summary stats
 - [[#797](https://github.com/nf-core/rnaseq/issues/797)] - Add `--skip_umi_extract` to account for pre-existing UMIs header embeddings.
 - [[#798](https://github.com/nf-core/rnaseq/issues/798)] - Decompress transcript fasta error
@@ -25,9 +27,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter                 | New parameter                         |
-|-------------------------------|---------------------------------------|
-|                               | `--skip_umi_extract`                  |
+| Old parameter | New parameter        |
+| ------------- | -------------------- |
+|               | `--skip_umi_extract` |
 
 ### Software dependencies
 

README.md

@@ -30,7 +30,7 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
 
 ## Pipeline summary
 
-![nf-core/RNASeq Workflow Diagram](docs/images/pipeline_diagram_grey.png)
+![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey.png)
 
 The SRA download functionality has been removed from the pipeline (`>=3.2`) and ported to an independent workflow called [nf-core/fetchngs](https://nf-co.re/fetchngs). You can provide `--nf_core_pipeline rnaseq` when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline.
 
@@ -59,7 +59,6 @@ The SRA download functionality has been removed from the pipeline (`>=3.2`) and
 15. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))
 
 > - **NB:** Quantification isn't performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.
-> - **NB:** The `--aligner star_rsem` option will require STAR indices built from version 2.7.6a or later. However, in order to support legacy usage of genomes hosted on AWS iGenomes the `--aligner star_salmon` option requires indices built with STAR 2.6.1d or earlier. Please refer to this [issue](https://github.com/nf-core/rnaseq/issues/498) for further details.
 
 ## Quick Start
 

bin/salmon_tximport.r

@@ -78,8 +78,8 @@ if(exists("gse")){
     write.table(build_table(gse.s, "counts"), paste(c(prefix, "gene_counts_scaled.tsv"), collapse="."), sep="\t", quote=FALSE, row.names = FALSE)
 }
 
-write.table(build_table(se,"abundance"), paste(c(prefix, "transcript_tpm.tsv"), collapse="."), sep="\t", quote=FALSE)
-write.table(build_table(se, "counts"), paste(c(prefix, "transcript_counts.tsv"), collapse="."), sep="\t", quote=FALSE)
+write.table(build_table(se,"abundance"), paste(c(prefix, "transcript_tpm.tsv"), collapse="."), sep="\t", quote=FALSE, row.names = FALSE)
+write.table(build_table(se, "counts"), paste(c(prefix, "transcript_counts.tsv"), collapse="."), sep="\t", quote=FALSE, row.names = FALSE)
 
 # Print sessioninfo to standard out
 citation("tximeta")

docs/usage.md

@@ -66,10 +66,12 @@ The minimum reference genome requirements are a FASTA and GTF file, all other fi
 - If `--gene_bed` is not provided then it will be generated from the GTF file.
 - If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
 
-When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568))
+When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568)).
 
 > **NB:** Compressed reference files are also supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension.
 
+As of v3.7 of the pipeline, if you are using a genome downloaded from AWS iGenomes and using `--aligner star_salmon` (default) the version of STAR to use for the alignment will be auto-detected (see [#808](https://github.com/nf-core/rnaseq/issues/808)).
+
 If you are using [GENCODE](https://www.gencodegenes.org/) reference genome files please specify the `--gencode` parameter because the format of these files is slightly different to ENSEMBL genome files:
 
 - The `--gtf_group_features_type` parameter will automatically be set to `gene_type` as opposed to `gene_biotype`, respectively.

nextflow_schema.json

@@ -98,7 +98,7 @@
                 "bbsplit_fasta_list": {
                     "type": "string",
                     "fa_icon": "fas fa-list-alt",
-                    "description": "Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit.",
+                    "description": "Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. You have to also explicitly set `--skip_bbsplit false` if you want to use BBSplit.",
                     "help_text": "The file should contain 2 columns: short name and full path to reference genome(s) e.g. \n```\nmm10,/path/to/mm10.fa\necoli,/path/to/ecoli.fa\n```"
                 },
                 "bbsplit_index": {