README.md



To learn more about this project, read the wiki.


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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


FULL EXAMPLE:

nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA


CHANGELOG


Credits
This workflow is was developed by Bioinformatic Core Facility (BICF), Department of Bioinformatics

PI
Venkat S. Malladi

Faculty Associate & Director

Bioinformatics Core Facility

UT Southwestern Medical Center

orcid.org/0000-0002-0144-0564

venkat.malladi@utsouthwestern.edu

Developers
Gervaise H. Henry

Computational Biologist

Department of Urology

UT Southwestern Medical Center

orcid.org/0000-0001-7772-9578

gervaise.henry@utsouthwestern.edu
Jonathan Gesell

Computational Biologist

Bioinformatics Core Facility

UT Southwestern Medical Center

orcid.org/0000-0001-5902-3299

johnathan.gesell@utsouthwestern.edu
Jeremy A. Mathews

Computational Intern

Bioinformatics Core Facility

UT Southwestern Medical Center

orcid.org/0000-0002-2931-1430

jeremy.mathews@utsouthwestern.edu
Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).


Pipeline Directed Acyclic Graph