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lilab-bcb · May 8, 2024 · 94f00a3 · 94f00a3
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diff --git a/docs/cellranger/build_refs.rst b/docs/cellranger/build_refs.rst
@@ -94,9 +94,9 @@ We provide a wrapper of ``cellranger mkref`` to build sc/snRNA-seq references. P
 		  - Ensembl v94
 		  -
 		* - cellranger_version
-		  - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
-		  - "7.1.0"
-		  - "7.1.0"
+		  - cellranger version, could be: 8.0.0, 7.2.0 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "8.0.0"
+		  - "8.0.0"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 
@@ -320,9 +320,9 @@ We provide a wrapper of ``cellranger mkvdjref`` to build single-cell immune prof
 		  - Ensembl v94
 		  -
 		* - cellranger_version
-		  - cellranger version, could be: 7.2.0, 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
-		  - "7.2.0"
-		  - "7.2.0"
+		  - cellranger version, could be: 8.0.0, 7.2.0, 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "8.0.0"
+		  - "8.0.0"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 

diff --git a/docs/cellranger/fixed_rna_profiling.rst b/docs/cellranger/fixed_rna_profiling.rst
@@ -15,6 +15,8 @@ Sample Sheet
           - Description
         * - **GRCh38-2020-A**
           - Human GRCh38 (GENCODE v32/Ensembl 98)
+        * - **mm10-2020-A**
+          - Mouse mm10 (GENCODE vM23/Ensembl 98)
 
 #. *DataType* column.
 

diff --git a/docs/cellranger/sc_sn_rnaseq.rst b/docs/cellranger/sc_sn_rnaseq.rst
@@ -13,6 +13,12 @@ Sample sheet
 
 		* - Keyword
 		  - Description
+		* - **GRCh38-2024-A**
+		  - Human GRCh38, comparable to cellranger reference 2024-A (GENCODE v44/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.*
+		* - **GRCm39-2024-A**
+		  - Mouse GRCm39, comparable to cellranger reference 2024-A (GENCODE vM33/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.*
+		* - **GRCh38_and_GRCm39-2024-A**
+		  - Human GRCh38 (v44/Ensembl 110) and mouse GRCm39 (GENCODE vM33/Ensembl 110). *Notice: This reference only supports Cell Ranger v6.0.0+.*
 		* - **GRCh38-2020-A**
 		  - Human GRCh38 (GENCODE v32/Ensembl 98)
 		* - **mm10-2020-A**

diff --git a/docs/spaceranger.rst b/docs/spaceranger.rst
@@ -71,10 +71,11 @@ Alternatively, users can submit jobs through command line interface (CLI) using
 		* - **Sample**
 		  - Contains sample names. Each 10x channel should have a unique sample name.
 		* - **Reference**
-		  -
-		  	| Provides the reference genome used by Space Ranger for each 10x channel.
-		  	| The elements in the *reference* column can be either Google bucket URLs to reference tarballs or keywords such as *GRCh38-2020-A*.
-		  	| A full list of available keywords is included in each of the following data type sections (e.g. sc/snRNA-seq) below.
+		  - Provides the reference genome used by Space Ranger for each 10x channel. The elements in the *reference* column can be either keywords of pre-built references or Google bucket URLs to reference tarballs. Below are available keywords of pre-built references:
+
+			- **GRCh38-2020-A**: Human GRCh38 (GENCODE v32/Ensembl 98)
+
+			- **mm10-2020-A**: Mouse mm10 (GENCODE vM23/Ensembl 98)
 		* - **Flowcell**
 		  -
 		    | Indicates the Google bucket URLs of uploaded BCL folders.
@@ -88,7 +89,17 @@ Alternatively, users can submit jobs through command line interface (CLI) using
 		* - **Index**
 		  - Sample index (e.g. SI-GA-A12).
 		* - ProbeSet
-		  - Probe set for FFPE samples. **Choosing** from ``human_probe_v1`` (10x human probe set, CytoAssist-incompatible), ``human_probe_v2`` (10x human probe set, CytoAssist-compatible) and ``mouse_probe_v1`` (10x mouse probe set). Alternatively, a CSV file describing the probe set can be directly used. Setting ProbeSet to ``""`` for a sample implies the sample is not FFPE.
+		  - Probe set for FFPE samples. Can be either a keyword or a cloud URI to a custom probe set. Below are keywords of available probe sets:
+
+		    - **human_probe_v2**: 10x human probe set version 2, CytAssist-compatible
+
+		    - **mouse_probe_v2**: 10x mouse probe set version 2, CytAssist-compatible
+
+		    - **human_probe_v1**: 10x human probe set version 1, CytAssist-compatible
+
+		    - **mouse_probe_v1**: 10x mouse probe set version 1, CytAssist-compatible
+
+		    **Notice:** Set ProbeSet to ``""`` for a sample implies the sample is not FFPE.
 		* - Image
 		  - Cloud bucket url for a brightfield tissue H&E image in .jpg or .tiff format. This column is mutually exclusive with DarkImage and ColorizedImage columns.
 		* - DarkImage