Yleaf module added @3.3.0 #8210
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This adds the Yleaf package (https://doi.org/10.1093/molbev/msy032) at 3.3.0. Currently locked to the local version while necessary Yleaf update is pending.
jfy133
reviewed
Apr 4, 2025
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def ref_genome = reference_genome ?: "hg38" | ||
| // These defaults correspond to the defaults used in the Yleaf package |
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Small comment: if the tool itself has it's own defaults then you don't need to define all of these. Input vals should ONLY be for mandatory inputs where there is no default 1
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| { assert process.out.versions != null }, | ||
| { assert process.out.haplogroup != null }, | ||
| { assert process.out.tree != null }, | ||
| { assert process.out.log != null } |
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Is this checking that teh file exists because they are variable? If so we have other patterns for this: https://nf-co.re/docs/contributing/nf-test/assertions
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In fact you don't need the != bit at all
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert process.out.versions != null }, |
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Suggested change
| { assert process.out.versions != null }, | |
| { assert process.out.versions }, |
Also all of these can go into a snapshot() function, so they are more explicitly recorded - see other modules for examples
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This adds the Yleaf package (https://doi.org/10.1093/molbev/msy032) at
3.3.0. Currently locked to the local version while necessary Yleaf
update is pending (genid/Yleaf#32)
Closes #8211.
PR checklist
Closes #XXX
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