Merge pull request #207 from grst/update-readme

update readme

Author: grst

README.md

@@ -4,8 +4,6 @@
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-
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@@ -28,6 +26,7 @@ This is a community effort in building a pipeline capable to support:
 - STARSolo
 - Kallisto + BUStools
 - Cellranger
+- UniverSC
 
 ## Documentation
 

docs/usage.md

@@ -50,12 +50,14 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 
 ### Expected cells
 
-This parameter may be used for three of the four supported aligning options.
+This parameter is currently supported by
 
 - [Salmon Alevin](https://salmon.readthedocs.io/en/latest/alevin.html#expectcells)
-- [Cellranger](https://software.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/release-notes) - NB: Current recommendation is to use auto-estimation of expected cells
 - [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md)
 
+In the future, support for this paramter will be added to cellranger and UniverSC. 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.