Resolve "Make instructions"

Closes #3 (closed)

README.md

@@ -10,4 +10,40 @@ The pipeline uses Nextflow, a bioinformatics workflow tool.
 
 This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.
 
-Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
\ No newline at end of file
+Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
+
+To Run:
+-------
+
+* Available parameters:
+  * **--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'**
+  * **--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'**
+    * **--genome**
+        * 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
+    * **--genomeLocationFull**
+    * **--expectCells**
+    * **--forceCells**
+    * **--kitVersion**
+    * **--version**
+    * **--outDir**
+
+* Design example:
+
+| Sample  | fastq_R1                           | fastq_R2                           |
+|---------|------------------------------------|------------------------------------|
+| sample1 | pbmc_1k_v2_S1_L001_R1_001.fastq.gz | pbmc_1k_v2_S1_L001_R2_001.fastq.gz |
+| sample2 | pbmc_1k_v2_S2_L001_R1_001.fastq.gz | pbmc_1k_v2_S2_L001_R2_001.fastq.gz |
+| sample2 | pbmc_1k_v2_S2_L002_R1_001.fastq.gz | pbmc_1k_v2_S2_L002_R2_001.fastq.gz |
\ No newline at end of file