--- title: nf-validate meeting brainstorming meeting tags: meeting, notes, nf-validate, brainstorming --- # nf-validate meeting brainstorming meeting Date: 2023-01-19 ## Attended Julia, Nicolas, Matthias H, Matthias dS, Edmund, @maxulysse ## Current status - Nextflow plugin to validate samplesheet **and** parameters - samplesheet schema inside parameter schema via inheritance - Based on work from @nvnieuwk: https://github.com/nvnieuwk/nf-samplesheet-conversion - CSV, TSV, YAML - Samplesheet schema (JSON schema) - Special entries: `meta` for building meta map - have to specify the name of the key the value will go in - Pattern checks (e.g. regex) - Specify nextflow file type - Can request to check that a field is unique within the whole sheet (across all rows of a column) - Currently: not possible _within_ 'groups' of rows - See also Phil's POC in rnaseq: https://github.com/nf-core/rnaseq/pull/623 ## Requests - Group based validation (e.g. no-duplicate lane IDs within a single sample name) - Add extra fields that we have for parameter validation. - Allow 'foreign' columns in the input sheet not required for the pipeline (that just get ignored/produce a warning) Good pipelines to check all functionality is covered - sarek - eager: https://github.com/nf-core/eager/blob/dev/bin/check_samplesheet.py ## Action List - Julia to prepare nf-core template to accept template - Nicolas to start converting existing lib/functions to plugin (https://github.com/nextflow-io/nf-validation)