Allow transcriptome-only salmon indexing #7327
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jfy133
reviewed
Jan 19, 2025
…ules into salmon_index_optional_genome
maxulysse
reviewed
Jan 20, 2025
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| { assert path(process.out.index.get(0)).exists() }, | ||
| { assert snapshot(process.out.versions).match("versions stub") } | ||
| { assert snapshot( | ||
| file(process.out.index[0]).listFiles().collect { it.getName() }.sort().toString(), | ||
| path(process.out.versions.get(0)).yaml | ||
| ).match()} |
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for stub you can do snapshot(process.out).match()
maxulysse
approved these changes
Jan 20, 2025
…ules into salmon_index_optional_genome
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Salmon indexing currently requires a genome as well as a transcriptome for Salmon indexing. We should provide for the possibility of transcritome-only indexing.
Working towards resolution of nf-core/rnaseq#688.
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