Merge pull request #1556 from nf-core/update_index_docs

Update index docs to remove references to 'indexing only mode'

Author: pinin4fjords

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1521](https://github.com/nf-core/rnaseq/pull/1521) - Updated Perl conda package version for local module gtf2bed for Arm compatibility.
 - [PR #1550](https://github.com/nf-core/rnaseq/pull/1550) - Simplify `SummarizedExperiment` outputs.
 - [PR #1553](https://github.com/nf-core/rnaseq/pull/1553) - Make jobs automatically resubmit for exit code 175
+- [PR #1556](https://github.com/nf-core/rnaseq/pull/1556) - Update index docs to remove references to 'indexing only mode'
 
 # 3.18.0 - 2024-12-19
 

docs/usage.md

@@ -138,10 +138,14 @@ Two additional parameters `--extra_star_align_args` and `--extra_salmon_quant_ar
 
 > **NB:** You can use `--skip_alignment --skip_pseudo_alignment` if you only want to run the pre-processing QC steps in the pipeline like FastQ, trimming etc. This will skip alignment, pseudoalignment and any post-alignment processing steps.
 
+Note that `--skip_alignment` and `--skip_pseudo_alignment` prevent both the execution of alignment/pseudoalignment steps and the building of their corresponding indices. For example, using `--skip_alignment` with `--aligner star_salmon` will skip both STAR alignment and index building.
+
 ## 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 pseudoalign and quantify your data with Salmon or Kallisto by providing the `--pseudo_aligner salmon` or `--pseudo_aligner kallisto` parameter, respectively.
 
+Note that `--skip_alignment` and `--skip_pseudo_alignment` affect both the execution of alignment/pseudoalignment steps and which indices are built during genome preparation. If you specify `--aligner star_salmon` but use `--skip_alignment`, the STAR index will not be built at all, as the skip parameter prevents both the index building and the alignment steps. This behavior helps save computational resources when you know you won't be using certain alignment methods.
+
 Since v3.0 of the pipeline, featureCounts is no longer used to perform gene/transcript quantification, however it is still used to generate QC metrics based on [biotype](http://www.ensembl.org/info/genome/genebuild/biotypes.html) information available within GFF/GTF genome annotation files. This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see [Zhao et al., 2015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001) and [Soneson et al., 2015](https://f1000research.com/articles/4-1521/v1).
 
 For similar reasons, quantification will not be performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments - this may change in future releases (see [#822](https://github.com/nf-core/rnaseq/issues/822)). HISAT2 has been made available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with it's output.
@@ -261,10 +265,7 @@ We recommend not providing a transcriptome FASTA file and instead allowing the p
 
 #### Indices
 
-By default, indices are generated dynamically by the workflow for tools such as STAR and Salmon. Since indexing is an expensive process in time and resources you should ensure that it is only done once, by retaining the indices generated from each batch of reference files:
-
-- the `--save_reference` parameter will save your indices in your results directory
-- the `--skip_alignment --skip_pseudo_alignment` will disable other processes if you'd like to do an 'indexing only' workflow run.
+By default, indices are generated dynamically by the workflow for tools such as STAR and Salmon. Since indexing is an expensive process in time and resources you should ensure that it is only done once, by retaining the indices generated from each batch of reference files by specifying `--save_reference`.
 
 Once you have the indices from a workflow run you should save them somewhere central and reuse them in subsequent runs using custom config files or command line parameters such as `--star_index '/path/to/STAR/index/'`.