Fix hisat2/align to support large genome indices (.ht2l) #9493
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This was referenced Dec 2, 2025
HISAT2 uses .ht2l extension instead of .ht2 for large genomes. Updated index detection to match both extensions. Related to nf-core/rnaseq#1643 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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- Update to latest upstream hisat2/align module which includes support for large genome indices (.ht2l extension) via nf-core/modules#9493 - Regenerate patch file for rnaseq-specific changes (contaminant_screening) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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HISAT2 uses .ht2l extension instead of .ht2 for large genomes. Updated index detection to match both extensions. Related to nf-core/rnaseq#1643 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude <[email protected]>
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Summary
HISAT2 uses
.ht2lextension instead of.ht2for large genome indices. The current module only detects.ht2indices, causing failures with large genomes.Changes
Updated the index detection command from:
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2$//'`To:
INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\.1.ht2.*$//'`This uses a wildcard glob to match both
.1.ht2and.1.ht2lextensions in a single pattern.Related
Related to nf-core/rnaseq#1643
Testing notes
Automated testing of large genome indices (
.ht2l) is not feasible because:hisat2-build.ht2files to.ht2ldoesn't work - the file formats are fundamentally differentManual verification: When
.ht2lfiles are present, the updatedfindcommand correctly:*.1.ht2lsedhisat2-align-l(the large-index variant)The existing tests continue to pass, verifying no regression for standard
.ht2indices.🤖 Generated with Claude Code