Migrate GRAPHMAP2_ALIGN to nf-test#8294
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SPPearce merged 4 commits intonf-core:masterfrom Apr 14, 2025
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I'm a bit concerned that the module isn't making usable sam files (but that seems to also be reflected in the github repo issues).
If it was a new module I'd ask for using samtools to make bam files, but not going to worry about that here.
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.versions, | ||
| // sam(process.out.sam[0][1]).getSamLinesMD5() htsjdk.samtools.SAMFormatException: Error parsing text SAM file. MAPQ must be zero if RNAME is not specified |
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Hmm, this feels a bit fishy that maybe the tool isn't making usable output files.
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I've open an issue on lbcb-sci/graphmap2#27
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* Migrate to nf-test * Add stub test * Remove comment
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PR checklist
Closes #7590
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda