Update README.md

README.md

@@ -24,73 +24,73 @@ To Run:
 
 * Available parameters:
   * **--fastq**
-        * path to the fastq location
-        * R1 and R2 only necessary but can include I2
-        * only fastq's in designFile (see below) are used, not present will be ignored
-        * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
+    * path to the fastq location
+    * R1 and R2 only necessary but can include I2
+    * only fastq's in designFile (see below) are used, not present will be ignored
+    * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
   * **--designFile**
-        * path to design file (csv format) location
-        * column 1 = "Sample"
-        * column 2 = "fastq_R1"
-        * column 3 = "fastq_R2"
-        * 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_count/blob/master/docs/design.csv)
-        * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv'**
-    * **--genome**
-        * reference genome
-        * requires workflow/conf/biohpc.config to work
-        * name of available 10x Gemomics premade reference genomes:
-            * *'GRCh38-3.0.0'* = Human GRCh38 release 93
-            * *'GRCh38-1.2.0'* = Human GRCh38 release 84
-            * *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
-            * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
-            * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 93
-            * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 84
-            * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
-            * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
-            * *'ercc92-1.2.0'* = ERCC.92 Spike-In
-        * if --genome is used then --genomeLocationFull is not necessary
-        * eg: **--genome 'GRCh38-3.0.0'**
-    * **--genomeLocationFull**
-        * path to a custom genome
-        * if --genomeLocationFull is used --genome is not necessary and is ignored
-        * eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
-    * **--expectCells**
-        * expected number of cells to be detected
-        * guides cellranger in it's cutoff for background/low quality cells
-        * as a guide it doesn't have to be exact
-        * 0-10000
-        * if --expextedCells is used then --forceCells is not necessary
-        * only used if --forceCells is not entered or set to 0
-        * eg: **--expectCells 10000**
-    * **--forceCells**
-        * forces filtering of the top number of cells matching this parameter
-        * 0-10000
-        * if --forceCells is used then --expectedCells is not necessary and is ignored
-        * eg: **--forceCells 10000**
-    * **--kitVersion**
-        * the library chemistry version number for the 10x Genomics Gene Expression kit
-        * setting to auto will attempt to autodetect from the detected sequencing strategy in the fastq's
-        * version numbers are spelled out
-        * --kitversion is only used if --version (cellranger version) is > 2
-        * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
-        * options:
-            * *'auto'*
-            * *'three'*
-            * *'two'*
-        * eg: **--kitVersion 'three'**
-    * **--version**
-        * cellranger version
-        * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
-        * options:
-            * *'3.0.2'*
-            * *'3.0.1'*
-            * *'2.1.1'*
-        * eg: **--version '3.0.2'**'
-    * **--outDir**
-        * optional output directory for run
-        * eg: **--outDir 'test'**
-    * FULL EXAMPLE:
+    * path to design file (csv format) location
+    * column 1 = "Sample"
+    * column 2 = "fastq_R1"
+    * column 3 = "fastq_R2"
+    * 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_count/blob/master/docs/design.csv)
+    * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv'**
+  * **--genome**
+    * reference genome
+    * requires workflow/conf/biohpc.config to work
+    * name of available 10x Gemomics premade reference genomes:
+        * *'GRCh38-3.0.0'* = Human GRCh38 release 93
+        * *'GRCh38-1.2.0'* = Human GRCh38 release 84
+        * *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
+        * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
+        * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 93
+        * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 84
+        * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
+        * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+        * *'ercc92-1.2.0'* = ERCC.92 Spike-In
+    * if --genome is used then --genomeLocationFull is not necessary
+    * eg: **--genome 'GRCh38-3.0.0'**
+  * **--genomeLocationFull**
+    * path to a custom genome
+    * if --genomeLocationFull is used --genome is not necessary and is ignored
+    * eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
+  * **--expectCells**
+    * expected number of cells to be detected
+    * guides cellranger in it's cutoff for background/low quality cells
+    * as a guide it doesn't have to be exact
+    * 0-10000
+    * if --expextedCells is used then --forceCells is not necessary
+    * only used if --forceCells is not entered or set to 0
+    * eg: **--expectCells 10000**
+  * **--forceCells**
+    * forces filtering of the top number of cells matching this parameter
+    * 0-10000
+    * if --forceCells is used then --expectedCells is not necessary and is ignored
+    * eg: **--forceCells 10000**
+  * **--kitVersion**
+    * the library chemistry version number for the 10x Genomics Gene Expression kit
+    * setting to auto will attempt to autodetect from the detected sequencing strategy in the fastq's
+    * version numbers are spelled out
+    * --kitversion is only used if --version (cellranger version) is > 2
+    * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+    * options:
+        * *'auto'*
+        * *'three'*
+        * *'two'*
+    * eg: **--kitVersion 'three'**
+  * **--version**
+    * cellranger version
+    * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+    * options:
+        * *'3.0.2'*
+        * *'3.0.1'*
+        * *'2.1.1'*
+    * eg: **--version '3.0.2'**
+  * **--outDir**
+    * optional output directory for run
+    * eg: **--outDir 'test'**
+* FULL EXAMPLE:
 
 **nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**