Update shapeit test and input tuple

[LouisLeNezet]

PR checklist

This PR do the following:

• Sort input for shapeit ligate and simplify its nf-test

• Input of shapeit phasecommon, phaserare and switch is now in one tuple to allow parallelization

• Extension for output for phasecommon is automatically detected

• Subworkflow :

  • Use glimpse2_chunk to create the chunk of each chromosome if not provided
  • The meta map is no more modified, allowing different usage

• 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

[pinin4fjords]

Just minor comments