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Fix: Migration changes for human_variant_annotation DAG
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afalam359 committed Nov 14, 2024
1 parent 5d8ed02 commit 2d8160a
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Showing 3 changed files with 38 additions and 18 deletions.
24 changes: 17 additions & 7 deletions datasets/human_variant_annotation/pipelines/clinvar/clinvar_dag.py
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Copyright 2021 Google LLC
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
Expand Down Expand Up @@ -38,8 +38,9 @@
task_id="clinvar_vcf_grch37",
startup_timeout_seconds=600,
name="name_basics",
namespace="composer",
service_account_name="datasets",
namespace="composer-user-workloads",
service_account_name="default",
config_file="/home/airflow/composer_kube_config",
image_pull_policy="Always",
image="{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}",
env_vars={
Expand All @@ -50,7 +51,11 @@
"TARGET_GCS_FOLDER": "data/human_variant_annotation/clinVar-vcf_GRCh37/",
"PIPELINE": "clinvar",
},
resources={"limit_memory": "1G", "limit_cpu": "1"},
container_resources={
"memory": {"request": "32Gi"},
"cpu": {"request": "2"},
"ephemeral-storage": {"request": "10Gi"},
},
)

# Task to run a GoogleCloudStorageToGoogleCloudStorageOperator
Expand All @@ -69,8 +74,9 @@
task_id="clinvar_vcf_grch38",
startup_timeout_seconds=600,
name="name_basics",
namespace="composer",
service_account_name="datasets",
namespace="composer-user-workloads",
service_account_name="default",
config_file="/home/airflow/composer_kube_config",
image_pull_policy="Always",
image="{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}",
env_vars={
Expand All @@ -81,7 +87,11 @@
"TARGET_GCS_FOLDER": "data/human_variant_annotation/clinVar-vcf_GRCh38/",
"PIPELINE": "db_snp",
},
resources={"limit_memory": "1G", "limit_cpu": "1"},
container_resources={
"memory": {"request": "32Gi"},
"cpu": {"request": "2"},
"ephemeral-storage": {"request": "10Gi"},
},
)

# Task to run a GoogleCloudStorageToGoogleCloudStorageOperator
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30 changes: 20 additions & 10 deletions datasets/human_variant_annotation/pipelines/clinvar/pipeline.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -35,8 +35,9 @@ dag:
task_id: "clinvar_vcf_grch37"
startup_timeout_seconds: 600
name: "name_basics"
namespace: "composer"
service_account_name: "datasets"
namespace: "composer-user-workloads"
service_account_name: "default"
config_file: "/home/airflow/composer_kube_config"
image_pull_policy: "Always"
image: "{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}"
env_vars:
Expand All @@ -46,9 +47,13 @@ dag:
GCS_BUCKET: "{{ var.value.composer_bucket }}"
TARGET_GCS_FOLDER: "data/human_variant_annotation/clinVar-vcf_GRCh37/"
PIPELINE: "clinvar"
resources:
limit_memory: "1G"
limit_cpu: "1"
container_resources:
memory:
request: "32Gi"
cpu:
request: "2"
ephemeral-storage:
request: "10Gi"

- operator: "GoogleCloudStorageToGoogleCloudStorageOperator"
description: "Task to run a GoogleCloudStorageToGoogleCloudStorageOperator"
Expand All @@ -67,8 +72,9 @@ dag:
task_id: "clinvar_vcf_grch38"
startup_timeout_seconds: 600
name: "name_basics"
namespace: "composer"
service_account_name: "datasets"
namespace: "composer-user-workloads"
service_account_name: "default"
config_file: "/home/airflow/composer_kube_config"
image_pull_policy: "Always"
image: "{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}"
env_vars:
Expand All @@ -78,9 +84,13 @@ dag:
GCS_BUCKET: "{{ var.value.composer_bucket }}"
TARGET_GCS_FOLDER: "data/human_variant_annotation/clinVar-vcf_GRCh38/"
PIPELINE: "db_snp"
resources:
limit_memory: "1G"
limit_cpu: "1"
container_resources:
memory:
request: "32Gi"
cpu:
request: "2"
ephemeral-storage:
request: "10Gi"

- operator: "GoogleCloudStorageToGoogleCloudStorageOperator"
description: "Task to run a GoogleCloudStorageToGoogleCloudStorageOperator"
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Copyright 2021 Google LLC
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
Expand Down

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