Update README.md

README.md

@@ -25,27 +25,27 @@ To Run:
 
 * Available parameters:
   * **--name**
-        * run name, puts outputs in a directory with this name
-        * eg: **--name 'test'**
+    * run name, puts outputs in a directory with this name
+    * eg: **--name 'test'**
   * **--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.
-        * eg: **--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'**
+    * 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.
+    * eg: **--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'**
   * **--designFile**
-        * path to design file (csv format) location
-        * column 1 = "Lane" (number of lanes to demultiplex, */** for all lanes)
-        * column 2 = "Sample" (sample name)
-        * column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
-        * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
-        * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
-        * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'**
-    * **--outDir**
-        * optional output directory for run
-        * eg: **--outDir 'test'**
-    * FULL EXAMPLE:
-
-**nextflow run workflow/main.nf --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'**
-
+    * path to design file (csv format) location
+    * column 1 = "Lane" (number of lanes to demultiplex, */** for all lanes)
+    * column 2 = "Sample" (sample name)
+    * column 3 = "Index" (10x sample index barcode, eg SI-GA-A1)
+    * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
+    * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
+    * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'**
+  * **--outDir**
+    * optional output directory for run
+    * eg: **--outDir 'test'**
+* FULL EXAMPLE:
+  ```
+  nextflow run workflow/main.nf --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'
+  ```
 * Design example:
 
 | Lane | Sample      | Index     |