{"id":13752249,"url":"https://github.com/aws-samples/aws-genomics-workflows","last_synced_at":"2025-05-09T18:33:31.885Z","repository":{"id":34701702,"uuid":"169794230","full_name":"aws-samples/aws-genomics-workflows","owner":"aws-samples","description":"Genomics Workflows on AWS","archived":true,"fork":false,"pushed_at":"2023-07-31T15:33:31.000Z","size":13005,"stargazers_count":145,"open_issues_count":0,"forks_count":110,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-03-14T11:02:34.432Z","etag":null,"topics":["aws","batch","genomics","step-functions","workflows"],"latest_commit_sha":null,"homepage":"https://docs.opendata.aws/genomics-workflows/","language":"Shell","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit-0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aws-samples.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-02-08T20:24:48.000Z","updated_at":"2025-01-16T03:09:12.000Z","dependencies_parsed_at":"2023-10-20T18:09:38.743Z","dependency_job_id":null,"html_url":"https://github.com/aws-samples/aws-genomics-workflows","commit_stats":null,"previous_names":[],"tags_count":37,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aws-samples%2Faws-genomics-workflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aws-samples%2Faws-genomics-workflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aws-samples%2Faws-genomics-workflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aws-samples%2Faws-genomics-workflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aws-samples","download_url":"https://codeload.github.com/aws-samples/aws-genomics-workflows/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253303308,"owners_count":21886919,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["aws","batch","genomics","step-functions","workflows"],"created_at":"2024-08-03T09:01:02.401Z","updated_at":"2025-05-09T18:33:26.921Z","avatar_url":"https://github.com/aws-samples.png","language":"Shell","funding_links":[],"categories":["Building","Ranked by starred repositories"],"sub_categories":["Workflows"],"readme":"# Genomics Workflows on AWS\n\n:warning: This site and related code are no longer actively maintained as of 2023-07-31. :warning:\n\nThis allows all code and assets presented here to remain publicly available for historical reference purposes only.\n\nFor more up to date solutions to running Genomics workflows on AWS checkout:\n\n- [Amazon Omics](https://aws.amazon.com/omics/) - a fully managed service for storing, processing, and querying genomic, transcriptomic, and other omics data into insights. [Omics Workflows](https://docs.aws.amazon.com/omics/latest/dev/workflows.html) provides fully managed execution of pre-packaged [Ready2Run](https://docs.aws.amazon.com/omics/latest/dev/service-workflows.html) workflows or private workflows you create using WDL or Nextflow.\n- [Amazon Genomics CLI](https://aws.amazon.com/genomics-cli/) - an open source tool that automates deploying and running workflow engines in AWS. AGC uses the same architectural patterns described here (i.e. operating workflow engines with AWS Batch). It provides support for running WDL, Nextflow, Snakemake, and CWL based workflows.\n\n---\n\nThis repository is the source code for [Genomics Workflows on AWS]().  It contains markdown documents that are used to build the site as well as source code (CloudFormation templates, scripts, etc) that can be used to deploy AWS infrastructure for running genomics workflows.\n\nIf you want to get the latest version of these solutions up and running quickly, it is recommended that you deploy stacks using the launch buttons available via the [hosted guide]().\n\nIf you want to customize these solutions, you can create your own distribution using the instructions below.\n\n## Creating your own distribution\n\nClone the repo\n\n```bash\ngit clone https://github.com/aws-samples/aws-genomics-workflows.git\n```\n\nCreate an S3 bucket in your AWS account to use for the distribution deployment\n\n```bash\naws s3 mb \u003cdist-bucketname\u003e\n```\n\nCreate and deploy a distribution from source\n\n```bash\ncd aws-genomics-workflows\nbash _scripts/deploy.sh --deploy-region \u003cregion\u003e --asset-profile \u003cprofile-name\u003e --asset-bucket s3://\u003cdist-bucketname\u003e test\n```\n\nThis will create a `dist` folder in the root of the project with subfolders `dist/artifacts` and `dist/templates` that will be uploaded to the S3 bucket you created above.\n\nUse `--asset-profile` option to specify an AWS profile to use to make the deployment.\n\n**Note**: the region set for `--deploy-region` should match the region the bucket `\u003cdist-bucketname\u003e` is created in.\n\nYou can now use your deployed distribution to launch stacks using the AWS CLI. For example, to launch the GWFCore stack:\n\n```bash\nTEMPLATE_ROOT_URL=https://\u003cdist-bucketname\u003e.s3-\u003cregion\u003e.amazonaws.com/test/templates\n\naws cloudformation create-stack \\\n    --region \u003cregion\u003e \\\n    --stack-name \u003cstackname\u003e \\\n    --template-url $TEMPLATE_ROOT_URL/gwfcore/gwfcore-root.template.yaml \\\n    --capabilities CAPABILITY_IAM CAPABILITY_AUTO_EXPAND \\\n    --parameters \\\n        ParameterKey=VpcId,ParameterValue=\u003cvpc-id\u003e \\\n        ParameterKey=SubnetIds,ParameterValue=\\\"\u003csubnet-id-1\u003e,\u003csubnet-id-2\u003e,...\\\" \\\n        ParameterKey=ArtifactBucketName,ParameterValue=\u003cdist-bucketname\u003e \\\n        ParameterKey=TemplateRootUrl,ParameterValue=$TEMPLATE_ROOT_URL \\\n        ParameterKey=S3BucketName,ParameterValue=\u003cstore-buketname\u003e \\\n        ParameterKey=ExistingBucket,ParameterValue=false\n\n```\n\n## Shared File System Support\n\nAmazon EFS is supported out of the box for `GWFCore` and `Nextflow`. You have two options to use EFS.\n\n1. **Create a new EFS File System:** Be sure to have `CreateEFS` set to `Yes` and also include the total number of subnets.\n2. **Use an Existing EFS File System:** Be sure to specify the EFS ID in the `ExistingEFS` parameter. This file system should be accessible from every subnet you specify.\n\nFollowing successful deployment of `GWFCore`, when creating your Nextflow Resources, set `MountEFS` to `Yes`.\n\n## Building the documentation\n\nThe documentation is built using mkdocs.\n\nInstall dependencies:\n\n```bash\n$ conda env create --file environment.yaml\n```\n\nThis will create a `conda` environment called `mkdocs`\n\nBuild the docs:\n\n```bash\n$ conda activate mkdocs\n$ mkdocs build\n```\n\n## License Summary\n\nThis library is licensed under the MIT-0 License. See the LICENSE file.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faws-samples%2Faws-genomics-workflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faws-samples%2Faws-genomics-workflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faws-samples%2Faws-genomics-workflows/lists"}