Closed kriemo closed 1 year ago
See https://github.com/nextflow-io/nextflow/discussions/3686
TLDR: add the nextflow.config
to the running directory and add executor.$local.cpus = 40 // or any other value of your choice
great, thanks for your help!
What happened?
I am trying to run this pipeline on a somewhat large 10x genomics 3' single cell library (~70Gb fastq.gz file). The pipeline errors when executing
pipeline:process_bams:stringtie
with the following message:I have set
max_threads
to24
on the command line. Here is the command run (with paths in the command and log altered for privacy).Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
No response
Workflow Execution - CLI Execution Profile
Singularity
Workflow Version
v0.1.8-g7f96b28
Relevant log output