Add new module: saltshaker/classify#10914
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ieduba merged 22 commits intonf-core:masterfrom Mar 17, 2026
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fellen31
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Mar 17, 2026
| type: file | ||
| description: tsv with classified call metadata to be used in saltshaker_plot | ||
| pattern: "*_classify_metadata.tsv" | ||
| ontologies: [] |
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I think there are ontologies for these.
| type: file | ||
| description: txt file with case classification | ||
| pattern: "*_classify.txt" | ||
| ontologies: [] |
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I think there are ontologies for these.
| type: file | ||
| description: vcf file with classified calls | ||
| pattern: "*saltshaker.vcf" | ||
| ontologies: [] |
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I think there are ontologies for these.
fellen31
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Mar 17, 2026
| """ | ||
| echo $args | ||
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| touch ${prefix}.saltshaker.vcf |
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Touch this only when --vcf is in args.
added 3 commits
March 17, 2026 10:48
…saltshaker_classify only make vcf in stub if vcf is in args
ctuni
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Mar 17, 2026
* add saltshaker classify module and tests * pin pip version * add saltshaker classify module and tests * pin pip version * update test with nf-core saltshaker/call * fix linting * add saltshaker classify module and tests * pin pip version * update test with nf-core saltshaker/call * fix linting * edits from review * update snaps and meta.yml * only make vcf in stub if vcf is in args * add no-vcf tests --------- Co-authored-by: Irene Duba <irene.duba@scilifelab.se>
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PR checklist
Add new module saltshaker/classify to build on the recently added module saltshaker/call. Together they perform downstream calling and classification of mitochondrial SVs from the mitosalt tool.
topic: versions- See version_topicslabelnf-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