Add ONT BAM and bedMethyl test data: HG002 GIAB 10-read subset (PAW70337)

[sahuno]

Summary

Adds 5 test data files derived from the GIAB HG002 ONT run PAW70337 (5kHz, R10.4.1), companion to the pod5 file merged in #1968.

New files

Unaligned BAM — raw dorado basecaller output, no reference:

• data/genomics/homo_sapiens/nanopore/bam/HG002_PAW70337_giab_10reads.unaligned.bam (178 KB)

Aligned sorted BAM + index — coordinate-sorted alignment to hg38 via minimap2:

• data/genomics/homo_sapiens/nanopore/bam/HG002_PAW70337_giab_10reads.aligned.sorted.bam (314 KB)
• data/genomics/homo_sapiens/nanopore/bam/HG002_PAW70337_giab_10reads.aligned.sorted.bam.bai (566 KB)

bedMethyl + tabix index — modkit pileup output (5mCG+5hmCG), bgzipped:

• data/genomics/homo_sapiens/nanopore/methylation/HG002_PAW70337_giab_10reads.aligned.sorted.bedmethyl.gz (69 KB)
• data/genomics/homo_sapiens/nanopore/methylation/HG002_PAW70337_giab_10reads.aligned.sorted.bedmethyl.gz.tbi (1.7 KB)

Modules that will use these files

File	Module(s)
unaligned.bam	dorado/summary, dorado/trim, dorado/correct
aligned.sorted.bam + .bai	modkit/pileup, dorado/basecaller functional test
bedmethyl.gz + .tbi	modkit/localize, modkit/localize/plot, modkit/pileup/plot

Source

s3://ont-open-data/giab_2025.01/flowcells/HG002/PAW70337/pod5/PAW70337_66b2eea5_de8117b1_33.pod5

• Sample: HG002 (NIST/Genome in a Bottle reference sample, public domain)
• Chemistry: 5kHz, R10.4.1 (PAW70337, released 2025-01-14)
• Subset: 10 reads — basecalled with dorado 1.4.0, aligned with minimap2, methylation called with modkit 0.6.1

Test plan

• BAM opens with samtools view
• BAI index validates with samtools idxstats
• bedMethyl decompresses and tabix queries correctly
• All files used in passing nf-test stub tests for the modules above

🤖 Generated with Claude Code

[sahuno]

Hey @dialvarezs 👋 , when you have a moment, could you pls review data inclusion pr?

This PR adds the unaligned/aligned HG002 BAM + bedMethyl test data (same GIAB 10-read subset as #1968, which you approved). It's the test-data dependency for two downstream module PRs:

• Add module: dorado/basecaller modules#11122 (dorado/basecaller — your current review)

• feat: add dorado/aligner module modules#11222 (dorado/aligner — new, draft)

  Happy to split or rescope if anything here is out of scope for the ONT test-data subdirectory.

Thanks!

[dialvarezs]

Hi @sahuno, sorry for the delay on this review.

Looking at the individual files, I think the unaligned BAM and aligned BAM + BAI make sense as reusable fixtures, especially if we want to avoid chaining through GPU-heavy dorado/basecaller steps.

The one I’m less sure about is the pre-generated bedmethyl.gz + .tbi, since that is already a downstream modkit pileup output. Would it be feasible to generate this via setup() from the aligned BAM for the other modkit tests instead? That way, we could preserve some chaining between dependent modules and help catch breaking changes more effectively over time.

[dialvarezs]

Also, what do you mean by "dorado/basecaller functional test`?