Version 2.1.0

CHANGELOG.md

-# v2.0.4
+# v2.1.0
 **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)
+* Attempt to prevent thredding error (which appears to only happen on 256GBv1 nodes)
 * Add option for 5' GEX chemistry
 * Remove cellranger 3.0.1 as an option
-* Add cellranger 2.2.0 as an option
 * Fix CLI MultiQC failure bug
 
 **Background**
 * Add Nextflow Tower integration into CI (GHH's profile)
 * Add new layered config folders, including prepare for awsifying
 * Update param to new standard
-* Use docker containers
 * Update CI
 * Add pipeline tracking tool
-* Add singularity to astrocyte workflow_modules
 
 *Known Bugs*
 * Vizapp does not yet work for Astrocyte

README.md

@@ -21,7 +21,10 @@ Additionally, the pipeline is designed to work with Astrocyte Workflow System us
 
 Cloud Compatibility
 -------------------
-This pipeline is also capable of being run on AWS. To do so:
+This pipeline is also capable of being run on AWS.
+**NOTE: This pipeline has been reverted to a non-containerized version to work on Astrocyte. Tag `containerized` for the last working containerized version which will be compatible with 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
@@ -35,6 +38,10 @@ To Run:
 -------
 
 * Available parameters:
+  * **-profile**
+    * what environments to run on, available: `biohpc`, `local`, `cluster`, `aws`, `ondemand`, `spot`
+    * eg: **-profile biohpc,cluster** to run on BioHPC in cluster mode
+    * eg: **-profile aws,ondemand** to run on AWS on a on-demand queue
   * **--fastq**
     * path to the fastq location
     * R1 and R2 only necessary but can include I2
@@ -95,11 +102,10 @@ To Run:
     * eg: **--kitVersion '3GEXv3'**
   * **--version**
     * cellranger version
-    * --version (cellranger version) 2.1.1 and 2.2.0 can only read --kitVersion of 3GEXv2
+    * --version (cellranger version) 2.1.1 can only read --kitVersion of 3GEXv2
     * options:
         * *'3.1.0'*
         * *'3.0.2'*
-        * *'2.2.0'*
         * *'2.1.1'*
     * eg: **--version '3.1.0'**
   * **--outDir**
@@ -107,7 +113,7 @@ To Run:
     * eg: **--outDir 'test'**
 * FULL EXAMPLE:
   ```
-  nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --outDir 'test'
+  nextflow run workflow/main.nf -profile biohpc,cluster --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --outDir 'test'
   ```
 * Design example:
 

workflow/main.nf

@@ -60,7 +60,7 @@ if (params.astrocyte) {
 params.genomeLocationFull = params.genomeLocation+params.genome
 
 // Define variables from input
-pipelineVersion = "2.x.x-indev"
+pipelineVersion = "2.1.0"
 name = params.name
 designLocation = Channel
   .fromPath(params.designFile)

workflow/nextflow.config

@@ -47,6 +47,6 @@ 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 = '2.x.x-indev'
+  version = '2.1.0'
   nextflowVersion = '>=0.31.0'
 }