From bc73cf592b635523d9551422c28df393eee58081 Mon Sep 17 00:00:00 2001 From: Gervaise Henry <GHENRY@swmed.org> Date: Mon, 17 Feb 2020 21:00:51 -0600 Subject: [PATCH] Update readme --- README.md | 38 +++++++++++++++++++++++++++++--------- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index c525c85..73b1175 100644 --- a/README.md +++ b/README.md @@ -13,17 +13,37 @@ This pipeline was created to be a standard mRNA-sequencing analysis pipeline whi  +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](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml) +* 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](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\ - note: 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) -* FULL EXAMPLE: - ``` - nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA - ``` + * ```--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)*** +* 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) + * *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 +``` @@ -33,7 +53,7 @@ To Run: Credits ======= -This worklow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/) +This workflow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/) PI -- -- GitLab