split the fastq and fastq_idx outputs from cellranger mkfastq module

[gordond88]

Issue: cellranger mkfastq outputs both fastq and fastq_idx files together which causes issues with some other processes (e.g. falco couldn't process index fastqs in the demultiplex pipeline).

Solution: split the fastq and fastq_idx outputs from cellranger mkfastq module.

PR checklist

Closes https://github.com/nf-core/demultiplex/pull/333

• [x] This comment contains a description of changes (with reason).
• [ ] Follow the input/output options guidelines.
• 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

[SPPearce]

Hi @gordond88 , you need to update the snapshots for the tests by running: nf-core modules test cellranger/mkfastq -u You'll also need to update the meta.yml file to reflect the fact you've added a new channel.

[SPPearce]

Closing in favour of #9204