The pipeline is failing almost immediately after launch because output folders for the tools are not being created. The initial file structure is properly created by the init command, and the run command correctly creates the first few output folders (sunbeam_output, sunbeam-output/logs, sunbeam_output/qc, sunbeam_output/qc/00-samples_intake), but then does not create any subsequent output folders, leading to the crash. The issue can be partially rectified by manually creating the output folder for a tool before the run, but the pipeline will then fail at the next step.
This is sunbeam v5.2.2 running slurm profile and occurs with both conda and git install
The pipeline is failing almost immediately after launch because output folders for the tools are not being created. The initial file structure is properly created by the init command, and the run command correctly creates the first few output folders (sunbeam_output, sunbeam-output/logs, sunbeam_output/qc, sunbeam_output/qc/00-samples_intake), but then does not create any subsequent output folders, leading to the crash. The issue can be partially rectified by manually creating the output folder for a tool before the run, but the pipeline will then fail at the next step.
This is sunbeam v5.2.2 running slurm profile and occurs with both conda and git install