FastQC uses only 10 cores in a 32 core server

[SuhasSrinivasan]

Description of feature

Despite specifying 32 cores through Slurm and Nextflow config, FastQC uses only 10 threads/cores, that is 1 thread per FASTQ file, even though there are more than 10 FASTQ files and 10 cores that can be utilized in parallel.

This behavior has been noticed with other tasks as well.

It will be very helpful if FastQC and other tools can use M threads = M FASTQ or intermediate files, where, M < N cores.

Max job request options
  max_cpus       : 32
  max_memory     : 240.GB

System information

Version of nf-core/atacseq: 2.1.2
Nextflow version: v24.10.3
Container enginer: Singularity
Executor: Slurm

[JoseEspinosa]

Could you share your configuration files? In principle fastQC should take 6 CPUs by running task as is labeled as process_medium see here and the resource declaration here, so not sure if you are overwriting this setting somehow.

[SuhasSrinivasan]

Thank you for reviewing.
As specified above, the nextflow.config was updated to use 32 cores.

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = '240.GB'
    max_cpus                   = 32
    max_time                   = '240.h'