@@ -9,7 +9,7 @@ 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.
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](https://portal.biohpc.swmed.edu)) at UT Southwestern Medical Center (in conjunction with the standard nextflow profile: config `biohpc.config`)
@@ -21,18 +21,19 @@ This pipeline is also capable of being run on AWS. To do so:
* 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
* 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](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
*```--bdbag``` active **cookies.txt** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
*```--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)***
*`--deriva` active **credential.json** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
*`--bdbag` active **cookies.txt** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
*`--repRID` mRNA-seq replicate RID
*`--refMoVersion` mouse reference version ***(optional)***
*`--refHuVersion` human reference version ***(optional)***
*`--refERCCVersion` human reference version ***(optional)***
*`-profile` config profile to use: standard = processes on 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](https://github.com/informatics-isi-edu/deriva-client#installer-packages-for-windows-and-macosx) 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)
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@@ -96,4 +97,4 @@ Please cite in publications: Pipeline was developed by BICF from funding provide
