FGBIO: GroupByUMI module fix

[FerriolCalvet]

Have you checked the docs?

• [X] nf-core website: troubleshooting
• [X] nf-core modules documentation

Description of the bug

The fgbio GroupByUMI module is missing a part of the configuration on how much memory to use. This bit is present in all the other fgbio modules but not in the GroupByUMI one, and I think it would be good to add it.

Although I have no knowledge on how GroupByUMI is using this information, it looks like it does not raise an error when using it and I guess it should adapt the amount of memory that it uses according to this parameter.

def mem_gb = 8
    if (!task.memory) {
        log.info '[fgbio FilterConsensusReads] Available memory not known - defaulting to 8GB. Specify process memory requirements to change this.'
    } else if (mem_gb > task.memory.giga) {
        if (task.memory.giga < 2) {
            mem_gb = 1
        } else {
            mem_gb = task.memory.giga - 1
        }
    }

....

        -Xmx${mem_gb}g \\

Command used and terminal output

No response

Relevant files

No response

System information

No response

[FerriolCalvet]

GroupReadsByUMI update

There is a new release of fgbio Release 2.2.0 In this release the execution of GroupReadsByUMI can be parallelized, even if it is only some internal steps and not the entire process it is worth having it updated. http://fulcrumgenomics.github.io/fgbio/tools/latest/GroupReadsByUmi.html