diff --git a/README.md b/README.md index ae33423a4719c29a91cb99d08fdf0dccd46308b0..f221d97744a0fb293e8c20d9dab4f8f57523954b 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: