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Update all examples
1 parent 7f6786b commit 86c98a7

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lines changed

‎examples/yaml/e2e/actions.yml

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@@ -9,4 +9,4 @@ actions:
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profile: 'test'
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params:
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outdir: s3://seqeralabs-showcase/nf-core-rnaseq/action/'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/compute-envs.yml

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@@ -14,16 +14,16 @@ compute-envs:
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no-ebs-auto-scale: True
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max-cpus: 500
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wait: AVAILABLE
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overwrite: True
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on_exists: overwrite
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- name: 'seqera_azure_virginia'
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workspace: 'seqerakit-e2e/showcase'
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credentials: 'azure_credentials'
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wait: 'AVAILABLE'
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file-path: './examples/yaml/compute-envs/seqera_azure_virginia.json'
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overwrite: True
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on_exists: overwrite
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- name: 'seqera_gcp_finland'
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workspace: 'seqerakit-e2e/showcase'
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credentials: 'google_credentials'
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wait: 'AVAILABLE'
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file-path: './examples/yaml/compute-envs/seqera_gcp_finland.json'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/credentials.yml

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@@ -4,31 +4,31 @@ credentials:
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workspace: 'seqerakit-e2e/showcase'
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username: 'ejseqera'
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password: '$TOWER_GITHUB_PASSWORD'
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overwrite: True
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on_exists: overwrite
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- type: 'container-reg'
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name: 'dockerhub_credentials'
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workspace: 'seqerakit-e2e/showcase'
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username: 'eshajoshi'
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password: '$DOCKERHUB_PASSWORD'
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registry: 'docker.io'
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overwrite: True
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on_exists: overwrite
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- type: 'aws'
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name: 'aws_credentials'
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workspace: 'seqerakit-e2e/showcase'
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access-key: '$AWS_ACCESS_KEY_ID'
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secret-key: '$AWS_SECRET_ACCESS_KEY'
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assume-role-arn: '$AWS_ASSUME_ROLE_ARN'
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overwrite: True
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on_exists: overwrite
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- type: 'azure'
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name: 'azure_credentials'
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workspace: 'seqerakit-e2e/showcase'
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batch-key: '$AZURE_BATCH_KEY'
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batch-name: 'seqeralabs'
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storage-key: '$AZURE_STORAGE_KEY'
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storage-name: 'seqeralabs'
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overwrite: True
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on_exists: overwrite
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- type: 'google'
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name: 'google_credentials'
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workspace: 'seqerakit-e2e/showcase'
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key: '$GOOGLE_KEY'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/datasets.yml

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@@ -4,28 +4,28 @@ datasets:
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/rnaseq_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'sarek_samples'
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description: 'Samplesheet to run the nf-core/sarek pipeline from end-to-end'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/sarek_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'viralrecon_illumina_samples'
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description: 'Samplesheet to run the nf-core/viralrecon pipeline from end-to-end with Illumina data'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/viralrecon_illumina_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'viralrecon_nanopore_samples'
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description: 'Samplesheet to run the nf-core/viralrecon pipeline from end-to-end with Nanopore data'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/viralrecon_nanopore_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'sentieon_samples'
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description: 'Samplesheet to run the seqeralabs/nf-sentieon pipeline from end-to-end'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/sentieon_samples.csv'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/labels.yml

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@@ -2,4 +2,4 @@ labels:
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- name: 'seqerakit'
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value: 'test'
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workspace: 'seqerakit-e2e/showcase'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/members.yml

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@@ -1,4 +1,4 @@
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members:
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- user: '[email protected]'
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organization: 'seqerakit-e2e'
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overwrite: False
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on_exists: ignore

‎examples/yaml/e2e/organizations.yml

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@@ -4,4 +4,4 @@ organizations:
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description: 'Organization created E2E with seqerakit CLI scripting'
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location: 'Global'
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website: 'https://seqera.io/'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/participants.yml

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@@ -3,9 +3,9 @@ participants:
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type: 'TEAM'
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workspace: 'seqerakit-e2e/showcase'
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role: 'ADMIN'
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overwrite: True
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on_exists: overwrite
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- name: '[email protected]'
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type: 'MEMBER'
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workspace: 'seqerakit-e2e/showcase'
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role: 'LAUNCH'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/pipelines.yml

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@@ -11,12 +11,12 @@ pipelines:
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outdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'
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config: './examples/yaml/pipelines/nextflow.config'
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pre-run: './examples/yaml/pipelines/pre_run.txt'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-core-sarek'
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workspace: 'seqerakit-e2e/showcase'
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compute-env: 'seqera_azure_virginia'
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file-path: './examples/yaml/pipelines/nf-core-sarek_pipeline.json'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-core-viralrecon-illumina'
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url: 'https://github.com/nf-core/viralrecon'
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workspace: 'seqerakit-e2e/showcase'
@@ -28,9 +28,9 @@ pipelines:
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params-file: './examples/yaml/pipelines/nf_core_viralrecon_illumina_params.yml'
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config: './examples/yaml/pipelines/nextflow.config'
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pre-run: './examples/yaml/pipelines/pre_run.txt'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-sentieon'
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workspace: 'seqerakit-e2e/showcase'
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compute-env: 'seqera_aws_virginia_fusionv2_nvme'
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file-path: './examples/yaml/pipelines/nf_sentieon_pipeline.json'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/secrets.yml

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@@ -2,4 +2,4 @@ secrets:
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- name: 'SENTIEON_LICENSE_BASE64'
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workspace: 'seqerakit-e2e/showcase'
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value: '$SENTIEON_LICENSE_BASE64'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/teams.yml

+1-1
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@@ -6,4 +6,4 @@ teams:
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- '[email protected]'
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- '[email protected]'
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- '[email protected]'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/e2e/workspaces.yml

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@@ -4,4 +4,4 @@ workspaces:
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organization: 'seqerakit-e2e'
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description: 'Workspace created E2E with seqerakit CLI scripting'
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visibility: 'PRIVATE'
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overwrite: True
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on_exists: overwrite

‎examples/yaml/seqerakit-e2e.yml

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@@ -4,7 +4,7 @@ organizations:
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description: 'Organization created E2E with seqerakit CLI scripting'
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location: 'Global'
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website: 'https://seqera.io/'
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overwrite: True
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on_exists: overwrite
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teams:
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- name: 'scidev_team'
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organization: 'seqerakit-e2e'
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- '[email protected]'
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- '[email protected]'
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- '[email protected]'
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overwrite: True
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on_exists: overwrite
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workspaces:
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- name: 'showcase'
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full-name: 'showcase'
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organization: 'seqerakit-e2e'
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description: 'Workspace created E2E with seqerakit CLI scripting'
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visibility: 'PRIVATE'
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overwrite: True
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on_exists: overwrite
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participants:
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- name: 'scidev_team'
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type: 'TEAM'
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workspace: 'seqerakit-e2e/showcase'
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role: 'ADMIN'
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overwrite: True
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on_exists: overwrite
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- name: '[email protected]'
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type: 'MEMBER'
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workspace: 'seqerakit-e2e/showcase'
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role: 'LAUNCH'
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overwrite: True
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on_exists: overwrite
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credentials:
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- type: 'github'
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name: 'github_credentials'
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workspace: 'seqerakit-e2e/showcase'
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username: 'ejseqera'
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password: '$TOWER_GITHUB_PASSWORD'
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overwrite: True
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on_exists: overwrite
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- type: 'container-reg'
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name: 'dockerhub_credentials'
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workspace: 'seqerakit-e2e/showcase'
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username: 'eshajoshi'
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password: '$DOCKERHUB_PASSWORD'
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registry: 'docker.io'
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overwrite: True
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on_exists: overwrite
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- type: 'aws'
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name: 'aws_credentials'
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workspace: 'seqerakit-e2e/showcase'
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access-key: '$AWS_ACCESS_KEY_ID'
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secret-key: '$AWS_SECRET_ACCESS_KEY'
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assume-role-arn: '$AWS_ASSUME_ROLE_ARN'
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overwrite: True
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on_exists: overwrite
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- type: 'azure'
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name: 'azure_credentials'
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workspace: 'seqerakit-e2e/showcase'
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batch-key: '$AZURE_BATCH_KEY'
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batch-name: 'seqeralabs'
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storage-key: '$AZURE_STORAGE_KEY'
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storage-name: 'seqeralabs'
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overwrite: True
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on_exists: overwrite
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- type: 'google'
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name: 'google_credentials'
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workspace: 'seqerakit-e2e/showcase'
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key: '$GOOGLE_KEY'
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overwrite: True
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on_exists: overwrite
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secrets:
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- name: 'SENTIEON_LICENSE_BASE64'
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workspace: 'seqerakit-e2e/showcase'
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value: '$SENTIEON_LICENSE_BASE64'
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overwrite: True
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on_exists: overwrite
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compute-envs:
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- type: aws-batch
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config-mode: forge
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no-ebs-auto-scale: True
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max-cpus: 500
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wait: AVAILABLE
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overwrite: True
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on_exists: overwrite
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- name: 'seqera_azure_virginia'
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workspace: 'seqerakit-e2e/showcase'
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credentials: 'azure_credentials'
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wait: 'AVAILABLE'
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file-path: './examples/yaml/compute-envs/seqera_azure_virginia.json'
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overwrite: True
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on_exists: overwrite
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- name: 'seqera_gcp_finland'
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workspace: 'seqerakit-e2e/showcase'
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credentials: 'google_credentials'
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wait: 'AVAILABLE'
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file-path: './examples/yaml/compute-envs/seqera_gcp_finland.json'
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overwrite: True
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on_exists: overwrite
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datasets:
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- name: 'rnaseq_samples'
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description: 'Samplesheet to run the nf-core/rnaseq pipeline from end-to-end'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/rnaseq_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'sarek_samples'
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description: 'Samplesheet to run the nf-core/sarek pipeline from end-to-end'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/sarek_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'viralrecon_illumina_samples'
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description: 'Samplesheet to run the nf-core/viralrecon pipeline from end-to-end with Illumina data'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/viralrecon_illumina_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'viralrecon_nanopore_samples'
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description: 'Samplesheet to run the nf-core/viralrecon pipeline from end-to-end with Nanopore data'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/viralrecon_nanopore_samples.csv'
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overwrite: True
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on_exists: overwrite
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- name: 'sentieon_samples'
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description: 'Samplesheet to run the seqeralabs/nf-sentieon pipeline from end-to-end'
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header: true
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workspace: 'seqerakit-e2e/showcase'
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file-path: './examples/yaml/datasets/sentieon_samples.csv'
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overwrite: True
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on_exists: overwrite
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pipelines:
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- name: 'nf-core-rnaseq'
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url: 'https://github.com/nf-core/rnaseq'
@@ -144,12 +144,12 @@ pipelines:
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outdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'
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config: './examples/yaml/pipelines/nextflow.config'
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pre-run: './examples/yaml/pipelines/pre_run.txt'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-core-sarek'
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workspace: 'seqerakit-e2e/showcase'
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compute-env: 'seqera_azure_virginia'
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file-path: './examples/yaml/pipelines/nf-core-sarek_pipeline.json'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-core-viralrecon-illumina'
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url: 'https://github.com/nf-core/viralrecon'
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workspace: 'seqerakit-e2e/showcase'
@@ -161,12 +161,12 @@ pipelines:
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params-file: './examples/yaml/pipelines/nf_core_viralrecon_illumina_params.yml'
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config: './examples/yaml/pipelines/nextflow.config'
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pre-run: './examples/yaml/pipelines/pre_run.txt'
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overwrite: True
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on_exists: overwrite
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- name: 'nf-sentieon'
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workspace: 'seqerakit-e2e/showcase'
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compute-env: 'seqera_aws_virginia_fusionv2_nvme'
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file-path: './examples/yaml/pipelines/nf_sentieon_pipeline.json'
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overwrite: True
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on_exists: overwrite
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launch:
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- name: 'nf-core-rnaseq-launchpad'
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workspace: 'seqerakit-e2e/showcase'

‎templates/actions.yml

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@@ -10,7 +10,7 @@ actions:
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profile: 'test' # optional
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params: # optional
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outdir: 's3://my_bucket/my_results'
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overwrite: True # optional
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on_exists: overwrite # optional
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- type: 'tower' # required
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name: 'my_tower_action' # required
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pipeline: 'https://github.com/my_username/my_repo' # required
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profile: 'test' # optional
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params: # optional
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outdir: 's3://my_bucket/my_results'
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overwrite: True # optional
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on_exists: overwrite # optional

‎templates/compute-envs.yml

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credentials: 'my_aws_credentials' # required
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wait: 'AVAILABLE' # optional
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file-path: './compute-envs/my_aws_compute_environment.json' # required
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overwrite: True # optional
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on_exists: overwrite # optional
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# To create a compute environment with options specified through YAML (AWS Example)
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- type: aws-batch # required
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config-mode: forge # required for AWS and Azure
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name: 'my_aws_compute_environment' # required
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workspace: 'my_organization/my_workspace' # optional
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credentials: 'my_aws_credentials' # required
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region: 'eu-west-1' # required
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region: 'eu-west-1' # required
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work-dir: 's3://my-bucket' # required
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provisioning-model: 'SPOT' # optional
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fusion-v2: False # optional
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wave: False # optional
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fargate: False # optional
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fast-storage: False # optional
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instance-types: 'c6i,r6i,m6i' # optional, comma separated list
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no-ebs-auto-scale: True # optional
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no-ebs-auto-scale: True # optional
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max-cpus: 500 # required
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labels: 'label1,label2' # optional, comma separated list
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vpc-id: 'vpc-1234567890' # optional
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vpc-id: 'vpc-1234567890' # optional
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subnets: 'subnet-1234567890,subnet-1234567891' # optional, comma separated list
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security-groups: 'sg-1234567890,sg-1234567891' # optional, comma separated list
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allow-buckets: 's3://my-bucket,s3://my-other-bucket' # optional, comma separated list
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wait: 'AVAILABLE' # optional
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overwrite: False # optional
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wait: 'AVAILABLE' # optional
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on_exists: ignore # optional

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