diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 24ec1953af2efca309526c6880cd28b17259f492..d74f92ba7ce1395d44b5fe431b7f6ecb85d164cb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,13 +15,13 @@ repos:
- id: check-merge-conflict
- id: check-ast
- repo: https://github.com/psf/black
- rev: 23.1.0
+ rev: 23.3.0
hooks:
- id: black
files: app
args: [--check]
- repo: https://github.com/charliermarsh/ruff-pre-commit
- rev: 'v0.0.257'
+ rev: 'v0.0.261'
hooks:
- id: ruff
- repo: https://github.com/pre-commit/mirrors-mypy
diff --git a/README.md b/README.md
index 875dee6a9c6c629a9bfc11ae5dd5271b40b2086c..81156fa33f8e3b8f8f156b94971499c590e003d9 100644
--- a/README.md
+++ b/README.md
@@ -25,16 +25,23 @@ This is the Workflow service of the CloWM service.
### Optional Variables
-| Variable | Default | Value | Description |
-|-----------------------------------|------------------------------|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|
-| `API_PREFIX` | `/api/workflow-service` | URL path | Prefix before every URL path |
-| `BACKEND_CORS_ORIGINS` | `[]` | json formatted list of urls | List of valid CORS origins |
-| `SQLALCHEMY_VERBOSE_LOGGER` | `False` | `<"True"|"False">` | Enables verbose SQL output.<br>Should be `false` in production |
-| `PARAMS_BUCKET` | `nxf-params` | Bucket Name | Bucket where the nextflow configurations for each execution should be saved |
-| `WORKFLOW_BUCKET` | `clowm-workflows` | Bucket Name | Bucket where to save important workflow files |
-| `ICON_BUCKET` | `clowm-icons` | Bucket name | Bucket where to save workflow icons. Should be publicly available. |
-| `SLURM_USER` | `slurm` | string | User on the slurm cluster who should run the job. Should be the user of the `SLURM_TOKEN` |
-| `SLURM_SHARED_DIR` | `/vol/spool/clowm-workflows` | Path on slurm cluster | Shared directory on the cluster where the nextflow jobs will be executed. |
-| `CONFIG_BUCKET_MOUNT_PATH` | `/mnt/config-bucket` | Path on slurm cluster | Folder where the S3 bucket `NFX_CONFIG_BUCKET` will be mounted on the slurm cluster |
-| `ACTIVE_WORKFLOW_EXECUTION_LIMIT` | `3` | Integer | Limit of active workflow execution a user is allowed to have. `-1` means infinite. |
-| `DEV_SYSTEM` | `False` | `<"True"|"False">` | Activates an endpoint that allows execution of an workflow from an arbitrary Git Repository.<br>HAS TO BE `False` in PRODUCTION! |
+| Variable | Default | Value | Description |
+|-----------------------------------|-------------------------|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|
+| `API_PREFIX` | `/api/workflow-service` | URL path | Prefix before every URL path |
+| `BACKEND_CORS_ORIGINS` | `[]` | json formatted list of urls | List of valid CORS origins |
+| `SQLALCHEMY_VERBOSE_LOGGER` | `False` | `<"True"|"False">` | Enables verbose SQL output.<br>Should be `false` in production |
+| `PARAMS_BUCKET` | `nxf-params` | Bucket Name | Bucket where the nextflow configurations for each execution should be saved |
+| `WORKFLOW_BUCKET` | `clowm-workflows` | Bucket Name | Bucket where to save important workflow files |
+| `ICON_BUCKET` | `clowm-icons` | Bucket name | Bucket where to save workflow icons. Should be publicly available. |
+| `SLURM_USER` | `slurm` | string | User on the slurm cluster who should run the job. Should be the user of the `SLURM_TOKEN` |
+| `PARAMS_BUCKET_MOUNT_PATH` | `/mnt/params-bucket` | Path on slurm cluster | Folder where the S3 bucket `PARAMS_BUCKET` will be mounted on the slurm cluster |
+| `ACTIVE_WORKFLOW_EXECUTION_LIMIT` | `3` | Integer | Limit of active workflow execution a user is allowed to have. `-1` means infinite. |
+| `DEV_SYSTEM` | `False` | `<"True"|"False">` | Activates an endpoint that allows execution of an workflow from an arbitrary Git Repository.<br>HAS TO BE `False` in PRODUCTION! |
+
+### Nextflow Variables
+
+All [Nextflow environment variables](https://www.nextflow.io/docs/latest/config.html#environment-variables) with the
+prefix `NXF_` are also support when submitting a job to the slurm cluster, e.g. pinning the Nextflow version
+```
+NXF_VER=23.04.0
+```
diff --git a/app/api/utils.py b/app/api/utils.py
index 25f0eb8010dc01e1877c33afc6d3da9025593ea6..4dde75e9e70b04ebadca126a038f89e6e0f9f0a5 100644
--- a/app/api/utils.py
+++ b/app/api/utils.py
@@ -109,7 +109,7 @@ async def start_workflow_execution(
nextflow_command = nextflow_command_template.render(
repo=git_repo,
params_file_name=params_file_name,
- config_mount_path=settings.CONFIG_BUCKET_MOUNT_PATH,
+ params_mount_path=settings.PARAMS_BUCKET_MOUNT_PATH,
execution_id=execution.execution_id,
report_output_bucket=report_output_bucket[5:]
if report_output_bucket is not None and report_output_bucket.startswith("s3://")
diff --git a/app/core/config.py b/app/core/config.py
index 4282d1fb61bd90e50f6d1ce9fedb946afafd11c3..bd12dc3c75183b5ef16cfe1ecdf08691174a5a7e 100644
--- a/app/core/config.py
+++ b/app/core/config.py
@@ -81,12 +81,8 @@ class Settings(BaseSettings):
SLURM_ENDPOINT: AnyHttpUrl = Field(..., description="URI of the Slurm Cluster")
SLURM_TOKEN: str = Field(..., description="JWT for authentication the Slurm REST API")
SLURM_USER: str = Field("slurm", description="User of communication with slurm")
- SLURM_SHARED_DIR: str = Field(
- "/vol/spool/clowm-workflows",
- description="Shared directory on the slurm cluster where the workflows will be executed",
- )
- CONFIG_BUCKET_MOUNT_PATH: str = Field(
- "/mnt/config-bucket", description="Path on the slurm cluster where the config bucket is mounted."
+ PARAMS_BUCKET_MOUNT_PATH: str = Field(
+ "/mnt/params-bucket", description="Path on the slurm cluster where the params bucket is mounted."
)
ACTIVE_WORKFLOW_EXECUTION_LIMIT: int = Field(3, description="The limit of active workflow executions per user.")
DEV_SYSTEM: bool = Field(False, description="Open a endpoint where to execute arbitrary workflows.")
diff --git a/app/slurm/slurm_rest_client.py b/app/slurm/slurm_rest_client.py
index be61d9d950254de6f82fa4c44ae5be69cd78d299..4e844d738a2a20817434e3a7b2733467f969c0bf 100644
--- a/app/slurm/slurm_rest_client.py
+++ b/app/slurm/slurm_rest_client.py
@@ -1,9 +1,14 @@
+from os import environ
from uuid import UUID
+import dotenv
from httpx import AsyncClient
from app.core.config import settings
+dotenv.load_dotenv()
+base_env = {key: val for key, val in environ.items() if key.startswith("NXF_")}
+
class SlurmClient:
def __init__(self, client: AsyncClient, version: str = "v0.0.38"):
@@ -37,16 +42,12 @@ class SlurmClient:
slurm_job_id : int
Slurm job ID of submitted job.
"""
- env = {
- "NXF_HOME": f"/home/{settings.SLURM_USER}/.nextflow",
- "NXF_WORK": settings.SLURM_SHARED_DIR,
- "NXF_ASSETS": settings.SLURM_SHARED_DIR,
- "TOWER_WORKSPACE_ID": execution_id.hex[:16],
- }
+ env = base_env.copy()
+ env["TOWER_WORKSPACE_ID"] = execution_id.hex[:16]
+
body = {
"script": nextflow_script,
"job": {
- "current_working_directory": settings.SLURM_SHARED_DIR,
"name": str(execution_id),
"requeue": False,
"environment": env,
diff --git a/mako_templates/nextflow_command.template b/mako_templates/nextflow_command.template
index 60fe5d99baf0751a6e653ea09f6ecbdf9a9adf13..e979690c9cfacac87b1709b2628c2f2c1465758e 100644
--- a/mako_templates/nextflow_command.template
+++ b/mako_templates/nextflow_command.template
@@ -7,4 +7,4 @@ nextflow run ${repo.repo_url} \
-with-timeline s3://${report_output_bucket}/timeline-${execution_id.hex}.html \
% endif
-revision ${repo.git_commit_hash} \
--params-file ${config_mount_path}/${params_file_name}
+-params-file ${params_mount_path}/${params_file_name}
diff --git a/requirements-dev.txt b/requirements-dev.txt
index aa771f8c386b253bc31402b39703ac90deedad39..7a2394487339991fad7f821895c0fa438a92a044 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,17 +1,16 @@
# test packages
pytest>=7.2.0,<7.3.0
-pytest-asyncio>=0.20.0,<0.21.0
+pytest-asyncio>=0.21.0,<0.22.0
pytest-cov>=4.0.0,<4.1.0
-coverage[toml]>=7.1.0,<7.2.0
+coverage[toml]>=7.2.0,<7.3.0
# Linters
ruff
-black>=23.01.0,<23.02.0
+black>=23.03.0,<23.04.0
isort>=5.12.0,<5.13.0
-mypy>=1.0.0,<1.1.0
+mypy>=1.1.0,<1.2.0
# stubs for mypy
boto3-stubs-lite[s3]>=1.26.0,<1.27.0
sqlalchemy2-stubs
types-requests
# Miscellaneous
-pre-commit>=3.1.0,<3.2.0
-python-dotenv
+pre-commit>=3.2.0,<3.3.0
diff --git a/requirements.txt b/requirements.txt
index 0e859b650103524be25b9ed3ee91e0c06e12249c..81318682c4711bb3b0627a59e18c8caec31801bf 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -21,3 +21,4 @@ httpx>=0.23.0,<0.24.0
itsdangerous
jsonschema>=4.0.0,<5.0.0
mako
+python-dotenv