MSIsensorPro output file name mismatch?

[DHelix]

Hi Sarek team,
Thanks again for all your work developing and maintaining Sarek!
I noticed a potential file name mismatch in the msisensorpro module.
In
~/.nextflow/assets/nf-core/sarek/modules/nf-core/msisensorpro/msisomatic/main.nf,
the output and stub blocks have two files named ${prefix}_germline and ${prefix}_somatic:

output:
    tuple val(meta), path("${prefix}")         , emit: output_report
    tuple val(meta), path("${prefix}_dis")     , emit: output_dis
    tuple val(meta), path("${prefix}_germline"), emit: output_germline, optional: true
    tuple val(meta), path("${prefix}_somatic") , emit: output_somatic,  optional: true
    path "versions.yml"                        , emit: versions

 stub:
    prefix   = task.ext.prefix ?: "${meta.id}"

    """
    touch ${prefix}
    touch ${prefix}_dis
    touch ${prefix}_germline
    touch ${prefix}_somatic

However, MSISensorPro v1.3.0 (used by Sarek 3.8.1) does not produce output files with these names. Instead, it generates files named ${prefix}_all and ${prefix}_unstable.
While ${prefix}_all and {prefix}_unstable are correctly generated, they are not captured by the workflow. Since the expected outputs are marked as optional, the process completes without error.

I’ve created a local patch to collect these outputs as a workaround. I thought it might be helpful to flag this in case the module could be updated in a future version of Sarek.

Thanks!

[SPPearce]

Hi @DHelix , this needs to be fixed in the nf-core/modules repository, as the modules are then pulled into sarek. So feel free to make a PR over there with this change (and tag me as a reviewer), and then it can get incorporated into sarek when we update the module here.