From cc90ce913384bdeaf5a97c8dfdcbd46f6b0a41b5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 14 Aug 2020 12:46:22 -0500
Subject: [PATCH] Update readme for vizFiles param
---
README.md | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/README.md b/README.md
index ae33423..f221d97 100755
--- a/README.md
+++ b/README.md
@@ -108,12 +108,17 @@ To Run:
* *'3.0.2'*
* *'2.1.1'*
* eg: **--version '3.1.0'**
+ * **--vizFiles**
+ * create objects which can be used for downstream visualization and analysis of each sample outputs, currently creates:
+ * Seurat R-objects
+ * true/false
+ * eg: **--version true**
* **--outDir**
* optional output directory for run
* eg: **--outDir 'test'**
* FULL EXAMPLE:
```
- nextflow run workflow/main.nf -profile biohpc,cluster --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --outDir 'test'
+ nextflow run workflow/main.nf -profile biohpc,cluster --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --vizFiles true --outDir 'test'
```
* Design example:
--
GitLab