Harden schema validation error messages and docs

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#155](https://github.com/nf-core/references/pull/155) - Added species-specific STAR index parameters (`--star_sjdbOverhang`, `--star_genomeSAindexNbases`) with per-genome asset file configuration
 - [#159](https://github.com/nf-core/references/pull/159) - Add release roadmap for rnaseq and sarek consumability
 - [#160](https://github.com/nf-core/references/pull/160) - Support list-valued VCF fields in datasheets, with positional TBI pairing (null entries trigger index building) and missing `ascat_loci_rt` schema entry
+- [#161](https://github.com/nf-core/references/pull/161) - Add `errorMessage` validation messages to `nextflow_schema.json` parameters
 
 ### Changed
 
@@ -62,6 +63,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#153](https://github.com/nf-core/references/pull/153) - Update modules
 - [#156](https://github.com/nf-core/references/pull/156) - Replace legacy `groupTuple` and `transpose` operators with `groupBy` and `flatMap`
 - [#157](https://github.com/nf-core/references/pull/157) - Replace `.out` channel access with typed workflow return assignment
+- [#161](https://github.com/nf-core/references/pull/161) - Document `references_base_path` description and igenomes prefix-rewriting behaviour
+- [#161](https://github.com/nf-core/references/pull/161) - Replace placeholder `TODO` error messages in `schema_references.json`
 
 ### Removed
 
@@ -74,6 +77,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#90](https://github.com/nf-core/references/pull/90) - Fixed link to GHA CI broken by [87](https://github.com/nf-core/references/pull/87)
 - [#141](https://github.com/nf-core/references/pull/141) - Fix snapaligner index generation when no alt liftover file is provided
 - [#149](https://github.com/nf-core/references/pull/149) - Fix params access
+- [#161](https://github.com/nf-core/references/pull/161) - Fix `input` mimetype from `text/csv` to `text/yaml`
 
 ### Dependencies
 

nextflow_schema.json

@@ -17,8 +17,9 @@
                     "format": "file-path",
                     "exists": true,
                     "schema": "subworkflows/local/utils_references/schema_references.json",
-                    "mimetype": "text/csv",
+                    "mimetype": "text/yaml",
                     "pattern": "^\\S+\\.(yaml|yml)$",
+                    "errorMessage": "Input datasheet must be an existing file ending in '.yaml' or '.yml' that does not contain spaces",
                     "description": "Path to yaml file containing information about the genome(s) and files to use for building references.",
                     "help_text": "You will need to create a datasheet with information about the genome(s) before running the pipeline. Use this parameter to specify its location. It has to be a yaml file. See [usage docs](https://nf-co.re/references/usage#datasheet).",
                     "fa_icon": "fas fa-file-csv"
@@ -34,26 +35,30 @@
                     "fa_icon": "fas fa-window-restore",
                     "description": "Select a predefined bundle of tools to build references for.",
                     "help_text": "Available bundles: 'all' (all available tools), 'rnaseq' (bowtie1, bowtie2, faidx, gffread, hisat2, hisat2_extractsplicesites, kallisto, rsem, rsem_make_transcript_fasta, salmon, sizes, star), 'sarek' (bwamem1, bwamem2, createsequencedictionary, dragmap, faidx, intervals, msisensorpro, snapaligner, tabix), 'null' (no tools). Can be combined with --tools and --skip_tools.",
-                    "pattern": "^((all|null|rnaseq|sarek)?,?)*(?<!,)$"
+                    "pattern": "^((all|null|rnaseq|sarek)?,?)*(?<!,)$",
+                    "errorMessage": "Tool bundle must be a comma-separated list of bundle names without spaces (e.g. rnaseq or rnaseq,sarek); available: all, rnaseq, sarek, null"
                 },
                 "tools": {
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Specify which tools to build references for.",
-                    "help_text": "Multiple tools separated with commas.",
-                    "pattern": "^((bowtie1|bowtie2|bwamem1|bwamem2|createsequencedictionary|dragmap|faidx|gffread|hisat2|hisat2_extractsplicesites|intervals|kallisto|msisensorpro|rsem|rsem_make_transcript_fasta|salmon|sizes|snapaligner|star|tabix)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas, without spaces (e.g. bwamem1,faidx).",
+                    "pattern": "^((bowtie1|bowtie2|bwamem1|bwamem2|createsequencedictionary|dragmap|faidx|gffread|hisat2|hisat2_extractsplicesites|intervals|kallisto|msisensorpro|rsem|rsem_make_transcript_fasta|salmon|sizes|snapaligner|star|tabix)?,?)*(?<!,)$",
+                    "errorMessage": "Tools must be a comma-separated list of valid tool names without spaces (e.g. bwamem1,faidx,star,tabix); see --help_full for the full list"
                 },
                 "skip_tools": {
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Specify which tools to skip building references for.",
-                    "help_text": "Multiple tools separated with commas.",
-                    "pattern": "^((bowtie1|bowtie2|bwamem1|bwamem2|createsequencedictionary|dragmap|faidx|gffread|hisat2|hisat2_extractsplicesites|intervals|kallisto|msisensorpro|rsem|rsem_make_transcript_fasta|salmon|sizes|snapaligner|star|tabix)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas, without spaces (e.g. hisat2,kallisto).",
+                    "pattern": "^((bowtie1|bowtie2|bwamem1|bwamem2|createsequencedictionary|dragmap|faidx|gffread|hisat2|hisat2_extractsplicesites|intervals|kallisto|msisensorpro|rsem|rsem_make_transcript_fasta|salmon|sizes|snapaligner|star|tabix)?,?)*(?<!,)$",
+                    "errorMessage": "Skipped tools must be a comma-separated list of valid tool names without spaces (e.g. hisat2,kallisto); see --help_full for the full list"
                 },
                 "references_base_path": {
                     "type": "string",
                     "format": "directory-path",
-                    "description": "The base path to the reference files",
+                    "description": "Base path used to resolve reference file paths in the datasheet, replacing the default 's3://ngi-igenomes/igenomes/' prefix.",
+                    "help_text": "Datasheets may carry igenomes-style 's3://ngi-igenomes/igenomes/...' paths. When this parameter is set, that prefix is rewritten to this base path before files are resolved, so you can point at a local or institutional mirror of igenomes without editing the datasheet.",
                     "fa_icon": "fas fa-ban"
                 },
                 "email": {
@@ -73,8 +78,7 @@
         "building_index_options": {
             "title": "Building index options",
             "type": "object",
-            "description": "",
-            "default": "",
+            "description": "Parameters controlling how reference indexes are built.",
             "properties": {
                 "kallisto_make_unique": {
                     "type": "boolean",
@@ -87,22 +91,25 @@
                     "description": "Length of donor and acceptor splice site anchors for the STAR splice junction database; typically 1 bp less than read length.",
                     "fa_icon": "fas fa-dna",
                     "help_text": "Typical values: 99 for mammals (100 bp reads), 74 for insects, 50-100 for plants. Overrides per-genome values from the input datasheet; falls back to STAR defaults when neither is set.",
-                    "minimum": 1
+                    "minimum": 1,
+                    "errorMessage": "STAR sjdbOverhang must be a positive integer"
                 },
                 "star_genomeSAindexNbases": {
                     "type": "integer",
                     "description": "Length of suffix array pre-indexing string for STAR genome indexing.",
                     "fa_icon": "fas fa-dna",
                     "help_text": "Typical values: 14 for large genomes (>500M bp), 11 for compact genomes (<300M bp). If not specified, calculated as log2(genome_size)/2-1, capped at 14. Overrides per-genome values from the input datasheet; falls back to STAR defaults when neither is set.",
                     "minimum": 1,
-                    "maximum": 14
+                    "maximum": 14,
+                    "errorMessage": "STAR genomeSAindexNbases must be an integer between 1 and 14"
                 },
                 "hisat2_build_memory": {
                     "type": "string",
                     "description": "Memory threshold for HISAT2 index building. When available process memory meets or exceeds this value, splice sites and exons are used to build a splice-aware index.",
                     "fa_icon": "fas fa-memory",
                     "default": "200.GB",
-                    "pattern": "^[0-9]+\\.?[0-9]*\\.?[GMK]B$"
+                    "pattern": "^[0-9]+\\.?[0-9]*\\.?[GMK]B$",
+                    "errorMessage": "HISAT2 build memory must be a memory value such as '200.GB', '3.GB' or '512MB'"
                 },
                 "hisat2_skip_splice_sites": {
                     "type": "boolean",

subworkflows/local/utils_references/schema_references.json

@@ -43,31 +43,31 @@
                 "meta": ["ascat_alleles"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "ASCAT alleles file must be a path that does not contain spaces"
             },
             "ascat_loci": {
                 "meta": ["ascat_loci"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "ASCAT loci file must be a path that does not contain spaces"
             },
             "ascat_loci_gc": {
                 "meta": ["ascat_loci_gc"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "ASCAT GC loci file must be a path that does not contain spaces"
             },
             "ascat_loci_rt": {
                 "meta": ["ascat_loci_rt"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "ASCAT RT loci file must be a path that does not contain spaces"
             },
             "bed12": {
                 "meta": ["bed12"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "BED12 file must be a path that does not contain spaces"
             },
             "bowtie1_index": {
                 "meta": ["bowtie1_index"],
@@ -108,7 +108,7 @@
                 "meta": ["chr_dir"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "Chromosome directory must be a path that does not contain spaces"
             },
             "fasta": {
                 "meta": ["fasta"],
@@ -175,13 +175,13 @@
             "macs_gsize": {
                 "meta": ["macs_gsize"],
                 "type": "number",
-                "errorMessage": "TODO"
+                "errorMessage": "MACS genome size must be a number (for example 1.2e7)"
             },
             "mito_name": {
                 "meta": ["mito_name"],
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "TODO"
+                "errorMessage": "Mitochondrial chromosome name must be a string value that does not contain spaces"
             },
             "msisensorpro_list": {
                 "meta": ["msisensorpro_list"],