Resolve "Make instructions"

Closes #3 (closed)

README.md

@@ -10,4 +10,85 @@ 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.
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+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/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/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'* = 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:
+
+| 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 |
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