diff --git a/igf_airflow/utils/dag50_olink_reveal_nextflow_utils.py b/igf_airflow/utils/dag50_olink_reveal_nextflow_utils.py index d1d2f24c..9d9685e1 100644 --- a/igf_airflow/utils/dag50_olink_reveal_nextflow_utils.py +++ b/igf_airflow/utils/dag50_olink_reveal_nextflow_utils.py @@ -155,10 +155,11 @@ def prepare_olink_nextflow_script( retries=4) def run_olink_nextflow_script(run_script: str): try: + script_dir = os.path.dirname(run_script) bash_cmd = f"""set -eo pipefail; -cd { os.path.dirname(run_script) }; -chmod u+x { run_script }; -bash { run_script }""" +cd {script_dir}; +chmod u+x {run_script}; +bash {run_script}""" return bash_cmd except Exception as e: log.error(e)