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!