Time limit of AlevinQC

[nictru]

Description of the bug

Currently, the time limit of AlevinQC is hard coded to 120h here since #196 was solved via #197. In my case, this led to Slurm PartitionTimeLimit problems (basically nothing was executed because the time limit of the queue is lower than 120h). Usually one can solve this by setting the max_time parameter. However, this parameter does not affect the AlevinQC time limit.

As an experienced nextflow user, one can easily find a temporary fix through adding this to nextflow.config:

process {
    withName: 'ALEVINQC' {
        time = '5.h'
    }
}

But I think figuring this out might be hard for users with less experience.

Some ideas for a permanent fix:

• Use the check_max function for setting the limit
• Assign one of the standard process labels (maybe process_low + process_long) and tell users to perform a manual override of the time limit if they really hit the time limit

I can also open a PR myself, but maybe I am missing something here, so let's discuss first

Command used and terminal output

No response

Relevant files

No response

System information

Slurm
nf-core/scrnaseq version 2.6.0

[grst]

Hi,

this should definitely use the check_max function. PR would be welcome!

[nictru]

Great, will open one later today!

[grst]

Closed by #335