Drop indev in version, finish adding aws details

CHANGELOG.md

-# v2.0.0 (in development)
+# v2.0.0
 **User Facing**
 * Check Design File for spaces in name and file contents
 * Attempt to preven thredding error (which appears to only happen on 256GBv1 nodes)

README.md

@@ -19,6 +19,18 @@ This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. Howe
 
 Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
 
+Cloud Compatibility
+-------------------
+This pipeline is also capable of being run on AWS. To do so:
+* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
+* Edit one of the aws configs in workflow/config/
+  * Replace workDir with the S3 bucket generated
+  * Change region if different
+  * Change queue to the aws batch queue generated
+* The user must be have awscli configured with an appropriate authentication (with ```aws configure``` and access keys) in the environment which nextflow will be run
+* Add ```-profile ``` with the name aws config which was custamized
+  * eg. ```nextflow run workflow/main.nf -profile aws_ondemand```
+
 To Run:
 -------
 

workflow/conf/aws.config

@@ -11,5 +11,34 @@ process {
   executor = 'awsbatch'
   queue = 'default-'
   cpus = 1
-  memory = '10 GB'
+  memory = '1 GB'
+
+  withLabel: checkDesignFile {
+    cpus = 2
+    memory = '1 GB'
+  }
+  withLabel: count211 {
+    cpus = 2
+    memory = '30 GB'
+  }
+  withLabel: count220 {
+    cpus = 2
+    memory = '30 GB'
+  }
+  withLabel: count302 {
+    cpus = 2
+    memory = '30 GB'
+  }
+  withLabel: count310 {
+    cpus = 2
+    memory = '30 GB'
+  }
+  withLabel: versions {
+    cpus = 3
+    memory = '1 GB'
+  }
+  withLabel: multiqc {
+    cpus = 1
+    memory = '1 GB'
+  }
 }

workflow/nextflow.config

@@ -62,6 +62,6 @@ manifest {
   homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
   description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
   mainScript = 'main.nf'
-  version = 'v2.0.0_indev'
+  version = 'publish_2.0.0'
   nextflowVersion = '>=0.31.0'
 }