From a1d75b8aee96a2760453cb1b9f6df447719a377c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 16 Apr 2020 09:46:18 -0500
Subject: [PATCH] Drop indev in version, finish adding aws details
---
CHANGELOG.md | 2 +-
README.md | 12 ++++++++++++
workflow/conf/aws.config | 31 ++++++++++++++++++++++++++++++-
workflow/nextflow.config | 2 +-
4 files changed, 44 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 186cd6d..d53ae5a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-# 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)
diff --git a/README.md b/README.md
index ab2141e..e8fe72a 100755
--- a/README.md
+++ b/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:
-------
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index e361237..6caee14 100644
--- a/workflow/conf/aws.config
+++ b/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'
+ }
}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 3e15f57..530f55b 100644
--- a/workflow/nextflow.config
+++ b/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'
}
--
GitLab