From cd3e90cb825b57856984d4949514342851a73830 Mon Sep 17 00:00:00 2001 From: chenv3 <43543446+chenv3@users.noreply.github.com> Date: Fri, 27 Dec 2024 17:53:52 -0500 Subject: [PATCH] Add Cell Ranger 9.0.0 to documentation, and integrate report copy rule to gex pipeline --- docs/usage/run.md | 16 ++++++++-------- workflow/rules/gex.smk | 14 +++++++++++++- .../scripts/seuratIntegrateSummaryReport.Rmd | 6 +++--- 3 files changed, 24 insertions(+), 12 deletions(-) diff --git a/docs/usage/run.md b/docs/usage/run.md index 66d03b2..e69a419 100644 --- a/docs/usage/run.md +++ b/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` diff --git a/workflow/rules/gex.smk b/workflow/rules/gex.smk index 2e0f59c..b4f34bb 100644 --- a/workflow/rules/gex.smk +++ b/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} + """ diff --git a/workflow/scripts/seuratIntegrateSummaryReport.Rmd b/workflow/scripts/seuratIntegrateSummaryReport.Rmd index 0ddda02..4686721 100755 --- a/workflow/scripts/seuratIntegrateSummaryReport.Rmd +++ b/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: "" ---