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<https://github.com/nf-core/test-datasets/pull/1969|#1969 Add ONT BAM and bedMethyl test data: HG002 GIAB 10-read subset (PAW70337)>
Pull request opened by <https://github.com/sahuno|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 <https://github.com/nf-core/test-datasets/pull/1968|#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
:robot_face: Generated with <https://claude.com/claude-code|Claude Code>
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>

Review on #1969 Add ONT BAM and bedMethyl test data: HG002 GIAB 10-read subset (PAW70337)
Review comment by <https://github.com/dialvarezs|dialvarezs> on <https://github.com/sahuno|sahuno's> pull request
Hi <@U0AJW45AMGE>, 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.
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>