Update glimpse2 imputation subworkflow

[LouisLeNezet]

PR checklist

Add genetic map in main tuple for GLIMPSE2_splitreference for parallelization purpose
Change glimpse2 imputation subworkflow from MULTIPLE to BAM_VCF to follow convention
Make chunking and reference split optional.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[LouisLeNezet]

Needs #9467 to be merged.

[pinin4fjords]

Again, this subscribe feels strange to me, and I don't see it used in other subworkflows. Could we use the same ifEmpty pattern?

[LouisLeNezet]

Sure I will do so before merging !

[LouisLeNezet]

I've changed it to

ch_chunks
            .filter { _meta, regionin, regionout -> regionin.size() == 0 && regionout.size() == 0 }
            .ifEmpty {
                error "ERROR: Cannot provide pre-defined chunks (regionin) when chunk=true. Please either set chunk=false to use provided chunks, or remove input chunks to enable automatic chunking."
            }

[pinin4fjords]

Approving to unblock you because I feel guilty for being distracted for a couple of days! Still wondering about the subscribe, but will leave you to resolve.

[LouisLeNezet]

Approving to unblock you because I feel guilty for being distracted for a couple of days! Still wondering about the subscribe, but will leave you to resolve.

No worries !
Is it better with this version ?

[pinin4fjords]

Approving to unblock you because I feel guilty for being distracted for a couple of days! Still wondering about the subscribe, but will leave you to resolve.

No worries ! Is it better with this version ?

You have my approval :-)