feat(cellranger/count): support SRA three-file FASTQ inputs (_1/_2/_3) in renaming logic

[emrunali]

Summary

This PR extends the cellranger count module’s FASTQ renaming logic to handle SRA / fasterq-dump outputs that produce three files per sample (*_1/_2/_3.fastq(.gz)), which is common for 10x chemistries when run with --split-files --include-technical.
Specifically:

• Detect SRA-style suffixes _1, _2, _3 in filenames.
• Group files by prefix and, when _2 and _3 are present, map:
  • _2 → R1 (barcode+UMI),
  • _3 → R2 (cDNA),
  • _1 (if present) → I1 (sample index).
• Keep existing behaviour for bcl2fastq-style R1/R2 filenames unchanged.
• Emit a clear error if neither pattern (bcl2fastq or SRA _1/_2/_3) can be recognised.
  No changes were required in modules/nf-core/cellranger/count/main.nf; all logic is contained within cellranger_count.py.

Motivation / use case

Many public 10x datasets are only available in SRA. When using:

prefetch SRR9304758
fasterq-dump --split-files --include-technical SRR9304758.sra

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[fmalmeida]

Hi @emrunali ,
Many thanks for the work in it.

The cellranger module is a nf-core module, thus the work / changes cannot happen directly in the pipeline side.

They should happen first in the modules repo, and then, the pipeline will only be modified to fetch the latest version.

So, I will not be accepting this PR so we can review in the correct repo .

😄

[emrunali]

Thanks @fmalmeida, will do as you suggested. 🙂