Add metabuli/build module #8148
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…date snapshot to exclude md5 comparison of db.parameters
jfy133
reviewed
Apr 17, 2025
| path taxonomy_nodes, stageAs: 'taxonomy/nodes.dmp' | ||
| path taxonomy_merged, stageAs: 'taxonomy/merged.dmp' | ||
| path accession2taxid, stageAs: 'taxonomy/*' | ||
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Missing optional --cds-info file
| Groovy Map containing sample information | ||
| - fasta: | ||
| type: file | ||
| description: Fasta file with input assemblies |
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Does it have to be a single fasta or can it be a list of FASTAs?
The docs imply to me that you can add lots of paths to fasta.txt?
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Yes - I think there is an option to provide multiple fastas to metabuli.
| description: File describing individual members of a taxonomic tree | ||
| - - taxonomy_nodes: | ||
| type: file | ||
| description: File describing parent-child relationships of a taxonomic tree |
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Suggested change
| description: File describing parent-child relationships of a taxonomic tree | |
| description: File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format |
I assume?
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| path("${process.out.db[0][1]}/acc2taxid.map"), | ||
| path("${process.out.db[0][1]}/diffIdx"), | ||
| path("${process.out.db[0][1]}/info"), | ||
| file("${process.out.db[0][1]}/split").name, | ||
| path("${process.out.db[0][1]}/taxID_list"), | ||
| file("${process.out.db[0][1]}/db.parameters").name, |
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If these are mostly files, you can include them in the stub run as empty fils with these names
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| } | ||
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PR checklist
Adds
metabuli/buildmodule that wrapsmetabuli build. Immediate need is having a possibility to use it innf-core/createtaxdbto later usemetabuli classifyinnf-core/taxprofilerCloses #8014
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