update README

README.md

@@ -4,13 +4,13 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2652611.svg)](https://doi.org/10.5281/zenodo.2652611)
 
-10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
+10x Genomics scRNA-Seq (cellranger/spaceranger) mkfastq Pipeline
 ==================================================
 
 Introduction
 ------------
 
-This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
+This pipeline is a wrapper for the cellranger or spaceranger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.
 
 FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.
 
@@ -42,11 +42,15 @@ To Run:
 * Available parameters:
   * **-profile**
     * what environments to run on, available: `biohpc`, `local`, `cluster`, `aws`, `ondemand`, `spot`
-    * eg: **-profile biohpc,cluster** to run on BioHPC in cluster mode
-    * eg: **-profile aws,ondemand** to run on AWS on a on-demand queue
+    * eg: ```-profile biohpc,cluster``` to run on BioHPC in cluster mode
+    * eg: ```-profile aws,ondemand``` to run on AWS on a on-demand queue
   * **--name**
     * run name, puts outputs in a directory with this name
-    * eg: **--name 'test'**
+    * eg: ```--name 'test'```
+  * **--ranger**
+    * select the 10x ranger being run.
+    * eg: ```--ranger 'cellranger'``` to run cellranger mkfastq
+    * eg: ```--ranger 'spaceranger'``` to run spaceranger mkfastq
   * **--bcl**
     * base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
     * there can be multiple basecall files, but they all will be demultiplexed by the same design file
@@ -63,13 +67,13 @@ To Run:
     * eg: ```--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'```
   * **--mask**
     * add a base mask if the sequencing strategy doesn't match the requirements of 10x Genomics
-    * eg: **--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'**
+    * eg: ```--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'```
   * **--outDir**
     * optional output directory for run
     * eg: ```--outDir 'test'```
 * FULL EXAMPLE:
   ```
-  nextflow run workflow/main.nf -profile biohpc,cluster --name 'test' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'
+  nextflow run workflow/main.nf -profile biohpc,cluster --name 'test' --ranger 'cellranger' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'
   ```
 * Design example: