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Generated with modkit pileup --phased --modified-bases 5mC 5hmC on the existing genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam fixture against genomics/homo_sapiens/genome/genome.fasta -- the same inputs and modified-bases args modkit/pileup's own --phased tests already use. test_hp1.bed.gz/test_hp2.bed.gz are the per-haplotype bedMethyl outputs, bgzip-compressed with a tabix index alongside each, as `modkit dmr pair` requires. Verified against a real `modkit dmr pair` run before committing. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Wit78XR11V9AMAgY7gGrMT
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Wit78XR11V9AMAgY7gGrMT
This was referenced Sep 23, 2026
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No longer needed, modkit/dmr's test now generates this fixture in-test via modkit/pileup, see nf-core/modules#13021 |
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Description
Adds data/genomics/homo_sapiens/nanopore/bedmethyl/{test_hp1,test_hp2}.bed.gz(.tbi), for testing the new modkit/dmr module (nf-core/modules#13021 (nf-core/modules#13021)).
modkit dmr pair compares two bgzip+tabix-indexed bedMethyl files. There's no bedmethyl fixture in this repo yet, but there is already a phased nanopore BAM (genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam) that modkit/pileup's own --phased tests use. I generated these two files by running:
modkit pileup --phased --modified-bases 5mC 5hmC
--ref genomics/homo_sapiens/genome/genome.fasta
--bgzf test.sorted.phased.bam test.tmp/
against that existing fixture (same reference, same --modified-bases args modkit/pileup's tests already use), then tabix-indexed the resulting per-haplotype outputs. No new BAM/FASTA needed, this reuses fixtures already in the repo.
Verified against a real modkit dmr pair run before submitting (not just that pileup succeeded).