Resolve "Set current directory"

.gitlab-ci.yml

@@ -115,11 +115,12 @@ lint-test-job: # Runs linters checks on code
   script:
     - ./scripts/lint.sh
 
-build-publish-dev-docker-container-job:
+publish-dev-docker-container-job:
   stage: deploy
   image:
     name: gcr.io/kaniko-project/executor:v1.9.1-debug
     entrypoint: [""]
+  dependencies: []
   only:
     refs:
       - development
@@ -132,11 +133,12 @@ build-publish-dev-docker-container-job:
       --destination "${CI_REGISTRY_IMAGE}:dev-${CI_COMMIT_SHA}"
       --destination "${CI_REGISTRY_IMAGE}:dev-latest"
 
-build-publish-docker-container-job:
+publish-docker-container-job:
   stage: deploy
   image:
     name: gcr.io/kaniko-project/executor:v1.9.1-debug
     entrypoint: [""]
+  dependencies: []
   only:
     - tags
   before_script:

README.md

@@ -37,6 +37,7 @@ This is the Workflow service of the CloWM service.
 | `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                                                  |
 | `NX_CONFIG`                       | unset                   | Path on slurm cluster       | Configuration file on the slurm cluster that is the same for every nextflow run                                                  |
 | `NX_BIN`                          | `nextflow`              | Path on slurm cluster       | Path to the nextflow executable. Default it is in the `PATH`                                                                     |
+| `SLURM_WORKING_DIRECTORY`         | `/tmp`                  | Path on slurm cluster       | Working directory for the slurm job with the nextflow command                                                                    |
 | `ACTIVE_WORKFLOW_EXECUTION_LIMIT` | `3`                     | Integer                     | Limit of active workflow execution a user is allowed to have. `-1` means infinite.                                               |
 | `DEV_SYSTEM`                      | `False`                 | `<"True"&#x7c;"False">`     | Activates an endpoint that allows execution of an workflow from an arbitrary Git Repository.<br>HAS TO BE `False` in PRODUCTION! |
 

app/core/config.py

@@ -86,6 +86,9 @@ class Settings(BaseSettings):
     )
     NX_CONFIG: str | None = Field(None, description="Path to a nextflow configuration for every run")
     NX_BIN: str = Field("nextflow", description="Path to the nextflow executable")
+    SLURM_WORKING_DIRECTORY: str = Field(
+        "/tmp", description="Working directory for the slurm job with the nextflow command"
+    )
     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.")
 

app/slurm/slurm_rest_client.py

@@ -49,6 +49,7 @@ class SlurmClient:
             "script": nextflow_script,
             "job": {
                 "name": str(execution_id),
+                "current_working_directory": settings.SLURM_WORKING_DIRECTORY,
                 "requeue": False,
                 "environment": env,
             },