Add ONT telomere test data (GIAB HG002)#1947
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pinin4fjords merged 1 commit intonf-core:modulesfrom Mar 24, 2026
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17 real telomeric ONT reads for testing telogator2 and other telomere analysis tools. Downsampled from GIAB 2025.01 ONT release (SUP basecalling, R10.4.1). Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
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Thanks @fellen31 ! |
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- tlens: tlens_by_allele.tsv (primary result) - plots: *.png (allele and violin plots, optional) - qc: qc directory (stats, read lengths, metadata) Also revert modules_testdata_base_path now that nf-core/test-datasets#1947 is merged. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
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* Add new module: telogator2 Add nf-core module for telogator2, a tool for allele-specific telomere length estimation and TVR characterization from long-read sequencing data (ONT/PacBio). Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * add telomere test data and temporarily point to fork - Add ONT telomere reads test (exercises real analysis path) - Keep PacBio no-telomere test (exercises graceful fallback) - Temporarily override modules_testdata_base_path to pinin4fjords/test-datasets#telogator2-test-data (revert before merge) Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: combine fasta and fai into single reference channel Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: simplify process script and assert failure on no telomere reads Remove error-catching wrapper from telogator2 process script. When no telomere reads are found the tool now fails with a clear error message, which the no-telomere test asserts against. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * refactor: emit individual files instead of directory - tlens: tlens_by_allele.tsv (primary result) - plots: *.png (allele and violin plots, optional) - qc: qc directory (stats, read lengths, metadata) Also revert modules_testdata_base_path now that nf-core/test-datasets#1947 is merged. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: exclude non-deterministic rng.txt from snapshot The qc/rng.txt file contains a random seed that differs across runs. Assert qc output exists but don't snapshot it. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: handle non-deterministic telogator2 outputs in tests Set fixed random seed (--rng 42) via test config. Assert tlens header structure rather than md5 since TL values vary across runs due to minimap2 non-determinism. Assert plots and qc exist without snapshotting. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: address PR review feedback - Use module_args pattern for ext.args in test config - Snapshot output file names (not md5s) for non-deterministic outputs - Remove PNGs from stub (plots are optional) Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * fix: make plots a required output The two main plots (all_final_alleles.png, violin_atl.png) are always produced on a successful run. Remove optional flag and add them back to the stub. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> * refactor: split QC directory into individual output channels Emit cmd, stats, qc_readlens, readlens, and rng as separate channels instead of a single qc directory. Touch all QC files in stub. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> --------- Co-authored-by: Claude Opus 4.6 (1M context) <[email protected]>
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Summary
data/genomics/homo_sapiens/nanopore/bam/HG002_ont_telomere/HG002_ont_tel_sub.bam(~491 KB) + indexContext
Needed for the new
telogator2nf-core module (nf-core/modules#11033). Existing PacBio test BAMs don't contain telomere reads, so telogator2 can only test its "no telomere reads" fallback path.🤖 Generated with Claude Code