README.md

master	develop

RNA-Seq Analytic Pipeline for GUDMAP/RBK

Introduction

This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.

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
• 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 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 customized

To Run:

• Available parameters:
  • --deriva active credential.json file from deriva-auth
  • --bdbag active cookies.txt file from deriva-auth
  • --repRID mRNA-seq replicate RID
  • --refMoVersion mouse reference version (optional)
  • --refHuVersion human reference version (optional)
  • -profile config profile to use: standard = local processes on BioHPC (default), biohpc = BioHPC cluster, aws_ondemand = AWS Batch on-demand instant requests, aws_spot = AWS Batch spot instance requests (optional)
• NOTES:
  • once deriva-auth is run and authenticated, the two files above are saved in ~/.deriva/ (see official documents from deriva on the lifetime of the credentials)
  • reference version consists of Genome Reference Consortium version, patch release and GENCODE annotation release # (leaving the params blank will use the default version tied to the pipeline version)
    • current mouse 38.p6.vM22 = GRCm38.p6 with GENCODE annotation release M22
    • current human 38.p6.v31 = GRCh38.p12 with GENCODE annotation release 31