Provide .fna support for pbmm2/align - #12602
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nvnieuwk
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Aug 6, 2026
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Some comments about the test, all other code looks good!
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Please add all tests to main.nf.test. This way all tests are in the same place which makes it easier to update them if necessary
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| test("sarscov2 - transcriptome fasta - stub") { | ||
| test("pbmm2 - bam - fna - stub") { |
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No need for a stub test here since there is already one in the main.nf.test
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Summary
Add support for reference files with the .fna extension when providing reference genomes to pbmm2.
Motivation
Many reference genomes distributed by NCBI and other bioinformatics resources use the .fna extension for FASTA-formatted nucleotide sequence files. While these files are standard FASTA files, pbmm2 currently does not recognize them as valid reference inputs. Therefore, users have to rename .fna files to .fa or .fasta before they can be used with pbmm2, even though the underlying file format is identical.
A corresponding issue has also been reported on the PacBio GitHub page: PacificBiosciences/pbbioconda#821
PR checklist
nf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda