Merge pull request #368 from an-altosian/dev

Update doc related to simpleaf, alevin-fry and salmon.

CITATIONS.md

@@ -18,6 +18,14 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [Simpleaf](https://doi.org/10.1093/bioinformatics/btad614)
+
+  > He, D., Patro, R. simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry, Bioinformatics 39, 10 (2023).
+
+* [Alevin-fry](https://doi.org/10.1038/s41592-022-01408-3)
+
+  > He, D., Zakeri, M., Sarkar, H. et al. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022).
+
 * [Alevin](https://doi.org/10.1186/s13059-019-1670-y)
 
   > Srivastava, A., Malik, L., Smith, T. et al. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biol 20, 65 (2019).

docs/output.md

@@ -9,20 +9,20 @@ This document describes the output produced by the pipeline. Most of the plots a
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [nf-core/scrnaseq: Output](#nf-corescrnaseq-output)
-  - [:warning: Please read this documentation on the nf-core website: https://nf-co.re/scrnaseq/output](#warning-please-read-this-documentation-on-the-nf-core-website-httpsnf-corescrnaseqoutput)
   - [Introduction](#introduction)
   - [Pipeline overview](#pipeline-overview)
   - [FastQC](#fastqc)
-  - [Kallisto & Bustools Results](#kallisto--bustools-results)
+  - [Kallisto \& Bustools Results](#kallisto--bustools-results)
   - [STARsolo](#starsolo)
-  - [Salmon Alevin & AlevinQC](#salmon-alevin--alevinqc)
+  - [Salmon \& Alevin-fry \& AlevinQC](#salmon--alevin-fry--alevinqc)
   - [Cellranger](#cellranger)
   - [Cellranger ARC](#cellranger-arc)
+  - [Cellranger multi](#cellranger-multi)
   - [UniverSC](#universc)
   - [Custom emptydrops filter](#custom-emptydrops-filter)
   - [Other output data](#other-output-data)
   - [MultiQC](#multiqc)
-  - [Pipeline information](#pipeline-information)
+    - [Pipeline information](#pipeline-information)
 
 ## FastQC
 
@@ -81,21 +81,23 @@ For details on how to load these into R and perform further downstream analysis,
 - `star_index`
   - Contains the index of the supplied genome fasta file
 
-## Salmon Alevin & AlevinQC
+## Salmon & Alevin-fry & AlevinQC
+
+This pipeline uses the simplified and flexible modules in [Simpleaf](https://simpleaf.readthedocs.io/en/latest/) for processing single-cell data with [Salmon](https://salmon.readthedocs.io/en/latest/) as the underlying mapper and [Alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) as the quantification tool. For detailed examples of using the quantification results generated by Alevin-fry in downstream analyses, such as RNA-velocity, please refer to [Alevin-fry/simpleaf tutorials](https://combine-lab.github.io/alevin-fry-tutorials/#blog).
 
 **Output directory: `results/alevin`**
 
 - `alevin`
-  - Contains the created Salmon Alevin pseudo-aligned output
+  - Contains the count matrix created by Alevin-fry
 - `alevinqc`
-  - Contains the QC report for the aforementioned Salmon Alevin output data
+  - Contains the QC report for the aforementioned Alevin-fry output data
 
 **Output directory: `results/reference_genome`**
 
 - `salmon_index`
-  - Contains the indexed reference transcriptome for Salmon Alevin
+  - Contains the indexed reference transcriptome for the Salmon mapper
 - `alevin/txp2gene.tsv`
-  - The transcriptome to gene mapping TSV file utilized by Salmon Alevin
+  - The transcriptome to gene mapping TSV file utilized by Alevin-fry
 
 ## Cellranger
 

docs/usage.md

@@ -39,15 +39,15 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 This parameter is currently supported by
 
-- [Salmon Alevin](https://salmon.readthedocs.io/en/latest/alevin.html#expectcells)
+- [Alevin-fry](https://alevin-fry.readthedocs.io/en/latest/generate_permit_list.html#:~:text=procedure%20described%20above.-,%2D%2Dexpect%2Dcells,-%3Cncells%3E%3A%20This)
 - [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md)
 - [Cellranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
 
 Note that since cellranger v7, it is **not recommended** anymore to supply the `--expected-cells` parameter.
 
 ## Aligning options
 
-By default, the pipeline uses [Salmon Alevin](https://salmon.readthedocs.io/en/latest/alevin.html) (i.e. --aligner alevin) to perform pseudo-alignment of reads to the reference genome and to perform the downstream BAM-level quantification. Then QC reports are generated with AlevinQC.
+By default (i.e. `--aligner alevin`), the pipeline uses [Salmon](https://salmon.readthedocs.io/en/latest/) to perform pseudo-alignment of reads to the reference genome and [Alevin-fry](https://alevin-fry.readthedocs.io/en/latest/) to perform the downstream BAM-level quantification. Then QC reports are generated with AlevinQC.
 
 Other aligner options for running the pipeline are:
 
@@ -100,11 +100,11 @@ The command `kb --list` shows all supported, preconfigured protocols. Additional
 
 For more details, please refer to the [Kallisto/bustools documentation](https://pachterlab.github.io/kallisto/manual#bus).
 
-#### Alevin/fry
+#### Alevin-fry
 
-Alevin/fry also supports custom chemistries in a slighly different format, e.g. `1{b[16]u[12]x:}2{r:}`.
+Simpleaf has the ability to pass custom chemistries to Alevin-fry, in a slighly different format, e.g. `1{b[16]u[12]x:}2{r:}`.
 
-For more details, see the [simpleaf documentation](https://simpleaf.readthedocs.io/en/latest/quant-command.html#a-note-on-the-chemistry-flag)
+For more details, see Simpleaf's paper, [He _et al._ 2023](https://doi.org/10.1093/bioinformatics/btad614).
 
 #### UniverSC
 

nextflow.config

@@ -22,7 +22,7 @@ params {
     fasta             = null
     gtf               = null
 
-    // salmon alevin parameters (simpleaf)
+    // alevin-fry parameters (simpleaf)
     simpleaf_rlen     = 91
     barcode_whitelist = null
     salmon_index      = null

nextflow_schema.json

@@ -59,7 +59,7 @@
                     "type": "string",
                     "description": "Name of the tool to use for scRNA (pseudo-) alignment.",
                     "default": "alevin",
-                    "help_text": "The workflow can handle three types of methods:\n\n- Kallisto/Bustools\n- Salmon Alevin + AlevinQC\n- STARsolo\n\nTo choose which one to use, please specify either `alevin`, `star` or `kallisto` as a parameter option for `--aligner`. By default, the pipeline runs the `alevin` option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.",
+                    "help_text": "The workflow can handle three types of methods:\n\n- Kallisto/Bustools\n- Salmon + Alevin-fry + AlevinQC\n- STARsolo\n\nTo choose which one to use, please specify either `alevin`, `star` or `kallisto` as a parameter option for `--aligner`. By default, the pipeline runs the `alevin` option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.",
                     "fa_icon": "fas fa-align-center",
                     "enum": ["kallisto", "star", "alevin", "cellranger", "universc", "cellrangerarc", "cellrangermulti"]
                 },
@@ -153,7 +153,7 @@
             }
         },
         "alevin_options": {
-            "title": "Alevin Options",
+            "title": "Alevin-fry Options",
             "type": "object",
             "description": "",
             "default": "",
@@ -167,8 +167,7 @@
                 },
                 "txp2gene": {
                     "type": "string",
-                    "description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.",
-                    "help_text": "> This is only used by the Salmon Alevin workflow.",
+                    "description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Alevin-fry and AlevinQC.",
                     "fa_icon": "fas fa-map-marked-alt",
                     "format": "file-path",
                     "exists": true