Fix nf-core#898

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#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.