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aws-samples / amazon-omics-tutorials

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Fix HISAT2_ALIGN to handle index files with trailing characters, e.g. ".ht2l" (l for Large) #58

Closed a1ultima closed 3 weeks ago

a1ultima commented 3 weeks ago

Description of changes:

On:

*/example-workflows/nf-core/workflows/rnaseq/modules/nf-core/hisat2/align/main.nf

Changed both occurrences of the following:

INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`

To:

INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`

Effect:

Correctly extend find's pattern match to capture both the standard *.ht2 named index files, as well as *.ht2l large genome index files e.g. Triticum Aestivum (genome from: ensembl/release-43/Triticum_aestivum.IWGSC.dna_sm.toplevel.fa.gz)