diff --git a/README.md b/README.md index fbb700ef12c3d006870dd8378741af9c5a404ca1..e2a78488d3dc1f4e605f593253697c28588a2909 100644 --- a/README.md +++ b/README.md @@ -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) @@ -96,4 +97,4 @@ Please cite in publications: Pipeline was developed by BICF from funding provide Pipeline Directed Acyclic Graph ------------------------------- - \ No newline at end of file +