Templates
Customize YAML configuration templates to use in seqerakit commands to create, update, or delete Seqera resources. Create or delete multiple resources with a single command by combining them into a single configuration file.
To use the templates on this page:
- Copy the template text or download the YAML files you need.
- Edit the values to specify your resource details, and save as a
.yamlfile. - Specify the YAML template file in your
seqerakitcommands:- To create the resources specified in the file:
seqerakit file.yaml- To delete the existing resources specified in the file:
seqerakit file.yaml --delete
info
See Specify targets to create or delete only selected resources from configuration templates that contain multiple resource entries.
See End-to-end example for a template that contains examples of all Seqera resources that can be created with Seqerakit.
Administration
Manage organizations, organization members, workspaces, teams, and participants.
Organizations
Add or delete organizations.
## To see the full list of options available, run: "tw organizations add -h"
organizations:
- name: 'your-organization' # required
full-name: 'Your Organization LLC' # required
description: 'Your organization description' # optional
location: 'Global' # optional
website: 'https://domain.com/' # optional
overwrite: True # optional
Members
Add or delete organization members.
## To see the full list of options available, run: "tw members add -h"
members:
- user: 'user@domain.com' # required
organization: 'your-organization' # required
overwrite: True # optional
Workspaces
Add or delete workspaces.
## To see the full list of options available, run: "tw workspaces add -h"
workspaces:
- name: 'workspace-1' # required
full-name: 'Workspace one' # required
organization: 'your-organization' # required
description: 'Your workspace description' # optional
visibility: 'PRIVATE' # optional
overwrite: True # optional
Teams
Add or delete teams.
## To see the full list of options available, run: "tw teams add -h"
teams:
- name: 'your-team' # required
organization: 'your-organization' # required
description: 'Your team description.' # optional
members: # optional
- 'team-member@domain.com'
overwrite: True # optional
Participants
Add or delete participants in workspaces and teams.
## To see the full list of options available, run: "tw participants add -h"
participants:
- name: 'your-team' # required
type: 'TEAM' # required
workspace: 'your-organization/workspace-1' # required
role: 'ADMIN' # required
- name: 'team-member@domain.com' # required
type: 'MEMBER' # required
workspace: 'your-organization/workspace-1' # required
role: 'LAUNCH' # required
Credentials
Add or delete compute environment, Git, and container registry credentials in workspaces.
## To see the full list of options available, run: "tw credentials add -h"
## To avoid exposing sensitive information about your credentials,
## use environment variables to supply passwords and secret keys.
credentials:
- type: 'github' # required
name: 'your-github-credentials' # required
workspace: 'your-organization/workspace-1' # required
username: 'your-username' # required
password: '$SEQPLATFORM_GITHUB_PASSWORD' # required
overwrite: True # optional
- type: 'container-reg' # required
name: 'your-dockerhub-credentials' # required
workspace: 'your-organization/workspace-1' # required
username: 'your-username' # required
password: '$DOCKERHUB_PASSWORD' # required
registry: 'docker.io' # required
overwrite: True # optional
- type: 'google' # required
name: 'your-google-credentials' # required
workspace: 'your-organization/workspace-1' # required
key: '$GOOGLE_KEY' # required
overwrite: True # optional
- type: 'aws' # required
name: 'your-aws-credentials' # required
workspace: 'your-organization/workspace-1' # required
access-key: '$AWS_ACCESS_KEY_ID' # required
secret-key: '$AWS_SECRET_ACCESS_KEY' # required
assume-role-arn: '$AWS_ASSUME_ROLE_ARN' # required
overwrite: True # optional
- type: 'azure' # required
name: 'your-azure-credentials' # required
workspace: 'your-organization/workspace-1' # required
batch-key: '$AZURE_BATCH_KEY' # required
batch-name: 'your-batch-name' # required
storage-key: '$AZURE_STORAGE_KEY' # required
storage-name: 'your-storage-name' # required
overwrite: True # optional
- type: 'codecommit' # required
name: 'your-codecommit-credentials' # required
workspace: 'your-organization/workspace-1' # required
access-key: '$CODECOMMIT_USER' # required
secret-key: '$CODECOMMIT_PASSWORD' # required
base-url: '$CODECOMMIT_BASEURL' # optional
overwrite: False # optional
Compute environments
Add or delete compute environments.
## To see the full list of options available, run: "tw compute-envs add -h"
## The options required to create compute environments can be specified:
## 1. Explicitly in this file
## 2. Via a JSON file exported from Seqera with the "tw compute-envs export" command
compute-envs:
# 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/aws_compute_environment.json' # required
overwrite: True # optional
# To create a compute environment with options specified through YAML (AWS Example)
- type: aws-batch # required
config-mode: forge # required for AWS and Azure (forge or manual)
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
Pipelines
Add or delete pipelines in workspace Launchpads.
## To see the full list of options available, run: "tw pipelines add -h"
## The options required to create pipelines can be specified:
## 1. Explicitly in this file
## 2. Via a JSON file exported from Seqera with the "tw pipelines export" command
pipelines:
- name: 'your-first-pipeline' # required
workspace: 'your-organization/workspace-1' # required
description: 'Options specified in this file' # optional
compute-env: 'your-aws-compute-environment' # required
work-dir: 's3://your-bucket' # optional
profile: 'test' # optional
revision: 'main' # required
params: # optional
outdir: 's3://your-bucket/results'
config: './pipelines/nextflow.config' # optional
pre-run: './pipelines/pre-run.txt' # optional
url: 'https://github.com/my_username/my_repo' # required
overwrite: True # optional
- name: 'your-second-pipeline' # required
workspace: 'your-organization/workspace-1' # required
description: 'Options specified via JSON file' # optional
compute-env: 'your-aws-compute-environment' # required
file-path: './pipelines/pipeline.json' # required
overwrite: True # optional
Launch
Launch a Nextflow pipeline.
## To see the full list of options available, run: "tw launch -h"
## The options will vary if you are launching a pipeline:
## 1. Pre-configured in the Seqera Launchpad with most options already specified
## 2. From source via a remote Git repository URL where you must explicitly specify all launch options
## Note: overwrite is not supported for "tw launch"
launch:
- name: 'launchpad-launch' # required
workspace: 'your-organization/workspace-1' # required
pipeline: 'nf-core-rnaseq' # required
params: # optional
outdir: 's3://your-bucket/results'
- name: 'remote-launch' # required
workspace: 'your-organization/workspace-1' # required
compute-env: 'your-aws-compute-environment' # required
pipeline: 'https://github.com/my_username/my_repo' # required
work-dir: 's3://your-bucket' # optional
profile: 'test' # optional
revision: 'main' # optional
params-file: './pipelines/params.yml' # optional
config: './pipelines/nextflow.config' # optional
pre-run: './pipelines/pre-run.txt' # optional
Datasets
Add or delete workspace datasets for pipeline input data.
## To see the full list of options available, run: "tw datasets add -h"
datasets:
- name: 'your-dataset' # required
description: 'Your dataset description' # optional
header: true # optional
workspace: 'your-organization/workspace-1' # required
file-path: './datasets/dataset.csv' # required
overwrite: True # optional
Labels
Add or delete labels and resource labels to apply to workspace compute environments, pipelines, and runs.
## To see the full list of options available, run: "tw labels add -h"
labels:
- name: 'label_name' # required
value: 'label_value' # required
workspace: 'your-organization/workspace-1' # required
overwrite: True # optional
Secrets
Add or delete user and workspace secrets.
## To see the full list of options available, run: "tw secrets add -h"
secrets:
- name: 'your-secret' # required
workspace: 'your-organization/workspace-1' # required
value: 'your-secret-value' # required
overwrite: True # optional
Actions
Add or delete pipeline actions.
## To see the full list of options available, run: "tw actions add -h"
actions:
- type: 'github' # required
name: 'your-github-action' # required
pipeline: 'https://github.com/my_username/my_repo' # required
workspace: 'your-organization/workspace-1' # required
compute-env: 'your-aws-compute-environment' # required
work-dir: 's3://your-bucket' # required
revision: 'main' # required
profile: 'test' # optional
params: # optional
outdir: 's3://your-bucket/results'
overwrite: True # optional
- type: 'tower' # required
name: 'your-tower-action' # required
pipeline: 'https://github.com/my_username/my_repo' # required
workspace: 'your-organization/workspace-1' # required
compute-env: 'your-aws-compute-environment' # required
work-dir: 's3://your-bucket' # required
revision: 'main' # required
profile: 'test' # optional
params: # optional
outdir: 's3://your-bucket/results'
overwrite: True # optional
End-to-end example
A template to create the following resources:
- An organization
- A workspace
- A team
- Participants
- Credentials
- Secrets
- Compute environments
- Datasets
- Pipelines
The template also contains launch entries to launch saved pipelines.
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