Resolve "Make instructions"

Closes #3 (closed)

README.md

@@ -19,26 +19,71 @@ To Run:
   * **--fastq**
         * path to the fastq location
         * R1 and R2 only necessary but can include I2
-        * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/\*.fastq.gz'**
+        * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/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 multiole fastq R1/R2 pairs for the samples
-        * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/design.csv'**
+        * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/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
-            * *'GRCh38-3.0.0'* = Human GRCh38 release 93
-            * *'GRCh38-3.0.0'* = Human GRCh38 release 93
-            * *'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'* = Human GRCm38 (mm10) release 93
+            * *'mm10-3.0.0'* = Human 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 overwritten
+        * 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 overwritten
+        * 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 cycle 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 main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**
 
 * Design example: