From a7609e0fccf4a070568d9beb0a7f6b0db2df6812 Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 27 Mar 2024 09:13:48 +0100 Subject: [PATCH] update params docs --- nextflow_schema.json | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index a837661d..1bc8a75a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -59,8 +59,8 @@ "format": "file-path", "mimetype": "text/tsv", "fa_icon": "fas fa-dna", - "description": "Path to tab-separated multi region sheet", - "help_text": "Path to multi region sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml).\n\nChoose a reerence taxonomy with `--sidle_ref_taxonomy` or use `--sidle_ref_tax_custom` and `--sidle_ref_tree_custom`.", + "description": "Path to multi-region definition sheet, for multi-region analysis with Sidle", + "help_text": "Path to file with information about sequenced regions, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml). This initiates scaffolding multiple regions along a reference.\n\nThe file must have four headers: \n- `region`: Unique region identifier\n- `region_length`: Minimal length of region\n- `FW_primer`: Forward primer sequence\n- `RV_primer`: Reverse primer sequence\n\nFor more details check the usage documentation.\n\nRelated parameters are:\n- `--sidle_ref_taxonomy` to select the reference taxonomic database\n- `--sidle_ref_tax_custom` for custom reference taxonomic database files\n- `--sidle_ref_tree_custom` for custom phylogenetic tree of reference taxonomic database", "schema": "assets/schema_multiregion.json" }, "outdir": { @@ -344,7 +344,8 @@ "taxonomic_database": { "title": "Taxonomic database", "type": "object", - "default": "Choose a method and database for taxonomic assignments to single-region amplicons", + "fa_icon": "fas fa-database", + "description": "Choose a method and database for taxonomic assignments to single-region amplicons", "properties": { "dada_ref_taxonomy": { "type": "string", @@ -541,13 +542,13 @@ "description": "Cutoff for partial ITS sequences. Only full sequences by default.", "default": 0 } - }, - "fa_icon": "fas fa-database" + } }, "multiregion_taxonomic_database": { "title": "Multi-region taxonomic database", "type": "object", - "default": "Choose database for taxonomic assignments with multi-region amplicons using SIDLE", + "fa_icon": "fas fa-database", + "description": "Choose database for taxonomic assignments with multi-region amplicons using SIDLE", "properties": { "sidle_ref_taxonomy": { "type": "string",