Assemble ONT genomes #516
Assemble ONT genomes #516
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fellen31
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| deepvariant_model_type = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO' | ||
| hifiasm_preset = params.preset == 'ONT_R10' ? '--ont' : '' | ||
| minimap2_read_mapping_preset = params.preset == 'ONT_R10' ? 'lr:hq' : 'map-hifi' |
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I am not sure I follow this part, if params.preset == 'ONT_R10' then hifiasm_preset = --ont, otherwise its empty, right? If so, won't whatever is given as a parameter --hifiasm_preset be overwritten?
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Yes, then it will be empty. However, it should be working the other way around, so whatever is given with --hifiasm_preset on the command line will overwrite what is set in nextflow.config ('' or --ont).
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ok, that makes sense then 😄
Perhaps it would be good to add a test?
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A test with --preset ONT_R10 is already there if that's what you mean, you can see the snapshot of the assembly outputs in tests/samplesheet_multisample_ont_bam.nf.test.snap.
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Sorry, yeah you are right, I was thinking more on the test config side, but if its there as an nf-core test, that should be enough
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Ah, okay. It would be nice, perhaps when I have fixed the stubs so we don't need to do it with a real run.
This parameter is not (edit) very likely to be changed on its own, but I double checked manually and --preset ONT_R10 results in the --ont flag being added to hifiasm, but --preset ONT_R10 --hifiasm_preset="" results in nothing added to hifiasm.
This PR updates hifiasm to 0.24.0, which adds beta support for ONT assembly with flag
--ont. Therefore assembly is now run by default with theONT_R10profile.Closes #515 and #518.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).