docs(modkit/pileup): clarify BAM index, BED format, and --cpg requirements

[sahuno]

Summary

• Update BAM index pattern from *.bai to *.{bai,csi} — modkit supports CSI indices via htslib, and ONT BAMs commonly use CSI
• Document that --include-bed requires strict BED3 or BED6 format — BED4 (e.g. UCSC CpG island downloads) is silently rejected, leading to a confusing "zero valid positions parsed" error
• Note that --cpg requires --modified-bases to also be passed via ext.args, otherwise modkit errors with "required arguments not provided"

All three issues were discovered while testing the module with real ONT methylation data (mm10, dorado basecalled BAMs with 5mCG_5hmCG modifications).

Changes

Documentation-only changes to meta.yml. No code changes to main.nf.

Test plan

• Verified module runs successfully with CSI-indexed BAMs via Nextflow on SLURM
• Verified --cpg --modified-bases 5mC produces correct bedMethyl output
• Verified BED3 input works after converting from BED4
• Existing nf-test suite should pass unchanged (no code modifications)

🤖 Generated with Claude Code

[SPPearce]

Please post on the nf-core slack #github-invitations channel, to be added to the organisation so the tests runs.

[SPPearce]

Is it worth adding a check in the module code itself for the --modified-bases or the number of columns in the bed file? Rather than just the meta.yml

[fellen31]

Is it worth adding a check in the module code itself for the --modified-bases or the number of columns in the bed file? Rather than just the meta.yml

For --modified-bases, I think the tool handles that pretty clearly already, i.e.:

error: the following required arguments were not provided:
  --modified-bases <MODIFIED_BASES>...

For better error reporting on the number of columns in the bed file, I feel like this is something that should be adressed in an issue at https://github.com/nanoporetech/modkit rather than checking it in the nf-core module. The tool is actively developed and maintained.