README.md



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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. 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)

Authentication:
The consortium server used must be authentificated with the deriva authentication client, and remain authentificated till the end of the pipeline run. Prematurely closing the client will result in invalidation of the tokens, and may result in the pipeline failure. The use of long-lived "globus" tokens is on the roadmap for use in the future.

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, default = 38.p6.vM25)


--refHuVersion human reference version (optional, default = 38.p13.v36)


--refERCCVersion human reference version (optional, default = 92)


--upload option to not upload output back to the data-hub (optional, default = false)


true = upload outputs to the data-hub

false = do NOT upload outputs to the data-hub


-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


--email email address(es) to send failure notification (comma separated) (optional):

e.g: --email 'Venkat.Malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'


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.vM25 = GRCm38.p6 with GENCODE annotation release M25

current human 38.p13.v36 = GRCh38.p13 with GENCODE annotation release 36


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/Q-Y5F6_inputBag_xxxxxxxx.zip (must be the expected bag structure, this example will not work because it is a test bag)


--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 a metadata mismatch or an ambiguous species error

eg: --speciesForce 'Mus musculus'


--strandedForce forces the strandedness to be "forward", "reverse" or "unstranded", it bypasses a metadata mismatch error

eg: --strandedForce 'unstranded'


--spikeForce forces the spike-in to be "false" or "true", it bypasses a metadata mismatch error

eg: --spikeForce 'true'


Tracking parameters (Tracking Site):


--ci boolean (default = false)

--dev boolean (default = true)


FULL EXAMPLE: