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. It is designed to run on the HPC cluster (BioHPC) at UT Southwestern Medical Center (in conjunction with the standard nextflow profile: config biohpc.config)

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
  • --source consortium server source
    • dev = dev.gudmap.org (default, does not contain all data)
    • staging = staging.gudmap.org (does not contain all data)
    • production = www.gudmap.org (does contain all data)
  • --refMoVersion mouse reference version (optional)
  • --refHuVersion human reference version (optional)
  • --refERCCVersion human reference version (optional)
  • -profile config profile to use (optional):
    • defaut = processes on BioHPC cluster
    • biohpc = process on BioHPC cluster
    • biohpc_max = process on high power BioHPC cluster nodes (=> 128GB nodes), for resource testing
    • aws_ondemand = AWS Batch on-demand instant requests
    • aws_spot = AWS Batch spot instance requests
• 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
• Optional input overrides
  • --refSource source for pulling references
    • biohpc = source references from BICF_Core gudmap reference local location (workflow must be run on BioHPC system)
    • datahub = source references from GUDMAP/RBK reference_table location (currently uses dev.gudmap.org)
  • --inputBagForce utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input)
    • eg: --inputBagForce test_data/bag/Replicate_Q-Y5F6.zip (must be the expected bag structure)
  • --fastqsForce utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
    • eg: --fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' (note the quotes around fastq's which must me named in the correct standard [*.R1.fastq.gz and/or *.R2.fastq.gz] and in the correct order)
  • --speciesForce forces the species to be "Mus musculus" or "Homo sapiens", it bypasses ambiguous species error
    • eg: --speciesForce 'Mus musculus'
• Tracking parameters (Tracking Site):
  • --ci boolean (default = false)
  • --dev boolean (default = false)