Remove fai index from bowtie2 modules

[Kevin-Brockers]

PR checklist

Removed the fai index from inputs in bowtie2 modules, updated corresponding modules, subworkflows and tests.

• This comment contains a description of changes (with reason).
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• 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
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker