Closed kostasgalexiou closed 9 months ago
Hi @kostasgalexiou, you can run the workflow with only either --fastq
or --bam
as input.
Also, please have a look at the Nextflow documentation for using it with SLURM (https://www.nextflow.io/docs/latest/executor.html#slurm). I'm not very familiar with SLURM, but I think your way of doing it will run Nextflow and all the processes it launches on the same node. If you want to use the cluster properly, you will need to add an extra config to your command (with nextflow run ... -c my-config
), which contains process.executor = 'slurm'
and cluster-specific options.
Please let us know if you run into any other issues.
Operating System
CentOS 7
Other Linux
No response
Workflow Version
v0.6.3-gc35c0ec
Workflow Execution
Other (please describe)
EPI2ME Version
No response
CLI command run
sbatch nextflow.sh
nextflow.sh file contents:
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I am running the test data for the alignment workflow. Process fails with an error regarding number of subschemas (see log output below).
Relevant log output
Application activity log entry
No response