Merge pull request #913 from drpatelh/fixes

FInal pre-release fixes

Author: drpatelh

CHANGELOG.md

@@ -10,9 +10,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Bump minimum Nextflow version from `21.10.3` -> `22.10.1`
 - Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
 - [[#729](https://github.com/nf-core/rnaseq/issues/729)] - Add 'auto' option to samplesheet to automatically detect strandedness for samples
+- [[#889](https://github.com/nf-core/rnaseq/issues/889)] - Document valid options for `--genome` parameter
 - [[#891](https://github.com/nf-core/rnaseq/issues/891)] - Skip MarkDuplicates when UMIs are used
 - [[#896](https://github.com/nf-core/rnaseq/issues/896)] - Remove `copyTo` call for iGenomes README
 - [[#897](https://github.com/nf-core/rnaseq/issues/897)] - Use `--skip_preseq` by default
+- [[#898](https://github.com/nf-core/rnaseq/issues/898)] - Documentation on salmon decoy-aware index creation, gcbias and seqbias
 - [[#900](https://github.com/nf-core/rnaseq/issues/900)] - Add `--recursive` option to `fastq_dir_to_samplesheet.py` script
 - [[#902](https://github.com/nf-core/rnaseq/issues/902)] - `check_samplesheet.py` script doesn't output optional columns in samplesheet
 - [[#907](https://github.com/nf-core/rnaseq/issues/907)] - Add `--extra_star_align_args` and `--extra_salmon_quant_args` parameter

docs/usage.md

@@ -57,6 +57,10 @@ By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `-
 
 You also have the option to pseudo-align and quantify your data with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) by providing the `--pseudo_aligner salmon` parameter. Salmon will then be run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon in isolation. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively. The library preparation protocol (library type) used by Salmon quantification is inferred by the pipeline based on the information provided in the samplesheet, however, you can override it using the `--salmon_quant_libtype` parameter. You can find the available options in the [Salmon documentation](https://salmon.readthedocs.io/en/latest/library_type.html).
 
+When running Salmon in mapping-based mode via `--pseudo_aligner salmon` the entire genome of the organism is used by default for the decoy-aware transcriptome when creating the indices (see second bulleted option in [Salmon documentation](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode)).
+
+Two additional parameters `--extra_star_align_args` and `--extra_salmon_quant_args` were added in v3.10 of the pipeline that allow you to append any custom parameters to the STAR align and Salmon quant commands, respectively. Note, the `--seqBias` and `--gcBias` are not provided to Salmon quant by default so you can provide these via `--extra_salmon_quant_args '--seqBias --gcBias'` if required.
+
 ## Quantification options
 
 The current options align with STAR and quantify using either Salmon (`--aligner star_salmon`) / RSEM (`--aligner star_rsem`). You also have the option to pseudo-align and quantify your data with Salmon by providing the `--pseudo_aligner salmon` parameter.
@@ -82,7 +86,9 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 
 ## Reference genome files
 
-The minimum reference genome requirements are a FASTA and GTF file, all other files required to run the pipeline can be generated from these files. However, it is more storage and compute friendly if you are able to re-use reference genome files as efficiently as possible. It is recommended to use the `--save_reference` parameter if you are using the pipeline to build new indices (e.g. those unavailable on [AWS iGenomes](https://nf-co.re/usage/reference_genomes)) so that you can save them somewhere locally. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space. You can then either provide the appropriate reference genome files on the command-line via the appropriate parameters (e.g. `--star_index '/path/to/STAR/index/'`) or via a custom config file.
+Please refer to the [nf-core website](https://nf-co.re/usage/reference_genomes) for general usage docs and guidelines regarding reference genomes.
+
+The minimum reference genome requirements for this pipeline are a FASTA and GTF file, all other files required to run the pipeline can be generated from these files. However, it is more storage and compute friendly if you are able to re-use reference genome files as efficiently as possible. It is recommended to use the `--save_reference` parameter if you are using the pipeline to build new indices (e.g. custom genomes that are unavailable on [AWS iGenomes](https://nf-co.re/usage/reference_genomes#custom-genomes)) so that you can save them somewhere locally. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space. You can then either provide the appropriate reference genome files on the command-line via the appropriate parameters (e.g. `--star_index '/path/to/STAR/index/'`) or via a custom config file.
 
 - If `--genome` is provided then the FASTA and GTF files (and existing indices) will be automatically obtained from AWS-iGenomes unless these have already been downloaded locally in the path specified by `--igenomes_base`.
 - If `--gff` is provided as input then this will be converted to a GTF file, or the latter will be used if both are provided.