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split the fastq and fastq_idx outputs from cellranger mkfastq module #8673

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@gordond88 gordond88 commented Jun 19, 2025

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 nf-core/demultiplex#333

  • 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

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.
@SPPearce
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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.

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