organizations: - name: 'your-organization' # required full-name: 'Your organization LLC' # required description: 'Organization created E2E with seqerakit CLI scripting' # optional location: 'Global' # optional website: 'https://yourdomain.com/' # optional overwrite: True # optional teams: - name: 'pipelines-team' # required organization: 'your-organization' # required description: 'Pipelines team @ Your organization' # optional members: # optional - 'user1@domain.com' - 'user2@domain.com' - 'user3@domain.com' overwrite: True # optional workspaces: - name: 'workspace-1' # required full-name: 'Workspace one' # required organization: 'your-organization' # required description: 'Workspace created E2E with seqerakit CLI scripting' # optional visibility: 'PRIVATE' # optional overwrite: True # optional participants: - name: 'pipelines-team' # required type: 'TEAM' # required workspace: 'your-organization/workspace-1' # required role: 'ADMIN' # required overwrite: True # optional - name: 'user@domain.com' # required type: 'MEMBER' # required workspace: 'your-organization/workspace-1' # required role: 'LAUNCH' # required overwrite: True # optional credentials: - type: 'github' # required name: 'github-credentials' # required workspace: 'your-organization/workspace-1' # required username: 'user1' # required password: '$TOWER_GITHUB_PASSWORD' # required overwrite: True # optional - type: 'container-reg' # required name: 'dockerhub-credentials' # required workspace: 'your-organization/workspace-1' # required username: 'user1' # required password: '$DOCKERHUB_PASSWORD' # required registry: 'docker.io' # required overwrite: True # optional - type: 'aws' # required name: 'aws-credentials' # required workspace: 'your-organization/workspace-1' # required access-key: '$AWS_ACCESS_KEY_ID' # required secret-key: '$AWS_SECRET_ACCESS_KEY' # required assume-role-arn: '$AWS_ASSUME_ROLE_ARN' # required overwrite: True # optional secrets: - name: 'SENTIEON_LICENSE_BASE64' # required workspace: 'your-organization/workspace-1' # required value: '$SENTIEON_LICENSE_BASE64' # required overwrite: True # optional compute-envs: # To create a compute environment with options specified through YAML (AWS Example) - type: aws-batch # required config-mode: forge # required for AWS and Azure name: 'your-aws-compute-environment' # required workspace: 'your-organization/workspace-1' # required credentials: 'your-aws-credentials' # required region: 'eu-west-1' # required work-dir: 's3://your-bucket' # required provisioning-model: 'SPOT' # optional fusion-v2: False # optional wave: False # optional fargate: False # optional fast-storage: False # optional instance-types: 'c6i,r6i,m6i' # optional, comma-separated list no-ebs-auto-scale: True # optional max-cpus: 500 # required labels: 'label1,label2' # optional, comma-separated list vpc-id: 'vpc-1234567890' # optional subnets: 'subnet-1234567890,subnet-1234567891' # optional, comma-separated list security-groups: 'sg-1234567890,sg-1234567891' # optional, comma-separated list allow-buckets: 's3://your-bucket,s3://your-other-bucket' # optional, comma-separated list wait: 'AVAILABLE' # optional overwrite: False # optional # To create a compute environment from a JSON configuration file (AWS Example) - name: 'your-aws-compute-environment' # required workspace: 'your-organization/workspace-1' # required credentials: 'your-aws-credentials' # required wait: 'AVAILABLE' # optional file-path: './compute-envs/your_aws_compute_environment.json' # required overwrite: True # optional datasets: - name: 'rnaseq_samples' # required description: 'Samplesheet to run the nf-core/rnaseq pipeline end-to-end' # optional header: true # optional workspace: 'your-organization/workspace-1' # required file-path: 'path/to/rnaseq_samples.csv' # required overwrite: True # optional pipelines: # To create a pipeline with options specified through YAML - name: 'nf-core-rnaseq' # required url: 'https://github.com/nf-core/rnaseq' # required workspace: 'your-organization/workspace-1' # required description: 'RNA sequencing analysis pipeline with gene/isoform counts and extensive quality control.' # optional compute-env: 'your-aws-compute-environment' # required work-dir: 's3://your-bucket/pipeline/working/directory' # optional profile: 'test' # optional revision: '3.12.0' # required params: # optional outdir: 's3://your-bucket/nf-core-rnaseq/results' config: 'path/to/nextflow.config' # optional pre-run: 'path/to/pipeline/pre_run.txt' # optional overwrite: True # optional # To create a pipeline from a JSON configuration file - name: 'nf-core-sarek' # required workspace: 'your-organization/workspace-1' # required compute-env: 'your-aws-compute-environment' # required file-path: 'path/to/nf-core-sarek_pipeline.json' # required overwrite: True # optional launch: # To launch a preconfigured pipeline from your workspace Launchpad - name: 'nf-core-rnaseq-launchpad' # required workspace: 'your-organization/workspace-1' # required pipeline: 'nf-core-rnaseq' # required compute-env: 'your-aws-compute-environment' # optional (defaults to workspace primary compute environment) # To launch an unsaved pipeline, include the pipeline repository URL and launch details - name: 'nf-core-rnaseq-remote' # required workspace: 'your-organization/workspace-1' # required pipeline: 'https://github.com/nf-core/rnaseq' # required compute-env: 'your-aws-compute-environment' # optional (defaults to workspace primary compute environment) work-dir: 's3://your-bucket/pipeline/working/directory' # optional profile: 'test' # optional revision: '3.12.0' # optional params-file: 'path/to/pipelines/nf_core_rnaseq_params.yml' # optional config: 'path/to/pipelines/nextflow.config' # optional pre-run: 'path/to/pipelines/pre_run.txt' # optional