Add Cell Ranger 9.0.0 to documentation, and integrate report copy rul…

…e to gex pipeline

docs/usage/run.md

@@ -78,11 +78,11 @@ Each of the following arguments are required. Failure to provide a required argu
 > ***Example:*** `--genome hg2024`
 
 ---  
-  `--cellranger {7.1.0, 7.2.0, 8.0.0}`
+  `--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
 > **The version of Cell Ranger to run.**   
 > *type: string*
 >   
-> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0
+> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
 >
 > ***Example:*** `--cellranger 7.1.0`
 
@@ -258,11 +258,11 @@ Each of the following arguments are required. Failure to provide a required argu
 > ***Example:*** `--genome hg38`
 
 ---  
-  `--cellranger {7.1.0, 7.2.0, 8.0.0}`
+  `--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
 > **The version of Cell Ranger to run.**   
 > *type: string*
 >   
-> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0
+> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
 >
 > ***Example:*** `--cellranger 7.1.0`
 
@@ -339,11 +339,11 @@ Each of the following arguments are required. Failure to provide a required argu
 > ***Example:*** `--genome hg38`
 
 ---  
-  `--cellranger {7.1.0, 7.2.0, 8.0.0}`
+  `--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
 > **The version of Cell Ranger to run.**   
 > *type: string*
 >   
-> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0
+> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
 >
 > ***Example:*** `--cellranger 7.1.0`
 
@@ -498,11 +498,11 @@ Each of the following arguments are required. Failure to provide a required argu
 > ***Example:*** `--genome hg38`
 
 ---  
-  `--cellranger {7.1.0, 7.2.0, 8.0.0}`
+  `--cellranger {7.1.0, 7.2.0, 8.0.0, 9.0.0}`
 > **The version of Cell Ranger to run.**   
 > *type: string*
 >   
-> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0
+> This option specifies which version of Cell Ranger to use when running GEX, VDJ, CITE, or MULTI pipelines. Please select one of the following options: 7.1.0, 7.2.0, 8.0.0, 9.0.0
 >
 > ***Example:*** `--cellranger 7.1.0`
 

workflow/rules/gex.smk

@@ -50,7 +50,7 @@ if len(samples) > 1:
   # Seurat Integration
   pipeline_output += [join(workpath, "seurat", "integrate", "integrated_sct.rds")]
   # Seurat Integration Report
-  pipeline_output += [join(workpath, "seurat", "integrate", "IntegrateOverviewReport.html")]
+  pipeline_output += [join(workpath, "finalreport", "seurat", "Integrate_Overview_Report.html")]
 
 
 # Cell Filter Summary File
@@ -447,3 +447,15 @@ rule seuratIntegrateSummaryReport:
 
         R -e "rmarkdown::render('{params.script}', params=list(seuratdir='{params.workdir}'), output_file='{output.report}')"
         """
+
+rule copySeuratIntegrateSummaryReport:
+  input:
+    report = rules.seuratIntegrateSummaryReport.output.report
+  output:
+    report = join(workpath, "finalreport", "seurat", "Integrate_Overview_Report.html")
+  params:
+    rname = "copySeuratIntegrateSummaryReport"
+  shell:
+    """
+    cp {input.report} {output.report}
+    """

workflow/scripts/seuratIntegrateSummaryReport.Rmd

@@ -1,6 +1,6 @@
 ---
-title: "Merge Integration Comparison"
-subtitle: ""
+title: "Seurat Merge and Integration Comparison"
+subtitle: "`r params$project`"
 author: "`r params$author`"
 output:
     rmdformats::html_clean:
@@ -14,7 +14,7 @@ output:
 date: "`r Sys.Date()`"
 params:
   seuratdir: seurat
-  project: Project
+  project: ""
   author: ""
 ---
 <style>