From 696d0dcfb47b27fedb0a7e0f3e98c0c905781a4f Mon Sep 17 00:00:00 2001 From: Luca Cinquini Date: Thu, 7 Mar 2024 11:07:13 -0700 Subject: [PATCH] [FIX] cwl-runner: error: argument --tmp-outdir-prefix: not allowed with argument --cachedir --- airflow/dags/docker_cwl_pod.yaml | 2 +- airflow/docker/cwl/docker_cwl_entrypoint.sh | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/airflow/dags/docker_cwl_pod.yaml b/airflow/dags/docker_cwl_pod.yaml index 31f1438f..d5354cfa 100644 --- a/airflow/dags/docker_cwl_pod.yaml +++ b/airflow/dags/docker_cwl_pod.yaml @@ -9,7 +9,7 @@ spec: containers: - name: cwl-docker # image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:2.0.0-alpha.1 - image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:develop6 + image: ghcr.io/unity-sds/unity-sps/sps-docker-cwl:develop7 imagePullPolicy: Always command: ["/usr/share/cwl/docker_cwl_entrypoint.sh"] securityContext: diff --git a/airflow/docker/cwl/docker_cwl_entrypoint.sh b/airflow/docker/cwl/docker_cwl_entrypoint.sh index bb2237bf..300e485d 100755 --- a/airflow/docker/cwl/docker_cwl_entrypoint.sh +++ b/airflow/docker/cwl/docker_cwl_entrypoint.sh @@ -44,8 +44,7 @@ done # Execute CWL workflow . /usr/share/cwl/venv/bin/activate pwd -mkdir -p ./cache -cwl-runner --cachedir ./cache --tmp-outdir-prefix "$PWD"/ "$cwl_workflow" "$job_args" +cwl-runner --tmp-outdir-prefix "$PWD"/ "$cwl_workflow" "$job_args" deactivate # Stop Docker engine