diff --git a/CHANGELOG.md b/CHANGELOG.md index bbc4125b..2dcb8981 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/nextflow_schema.json b/nextflow_schema.json index ce419de3..a332051a 100644 --- a/nextflow_schema.json +++ b/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)$", + "errorMessage": "Input datasheet must be an existing file ending in '.yaml' or '.yml' that does not contain spaces", "description": "Path to yaml file containing information about the genome(s) and files to use for building references.", "help_text": "You will need to create a datasheet with information about the genome(s) before running the pipeline. Use this parameter to specify its location. It has to be a yaml file. See [usage docs](https://nf-co.re/references/usage#datasheet).", "fa_icon": "fas fa-file-csv" @@ -34,26 +35,30 @@ "fa_icon": "fas fa-window-restore", "description": "Select a predefined bundle of tools to build references for.", "help_text": "Available bundles: 'all' (all available tools), 'rnaseq' (bowtie1, bowtie2, faidx, gffread, hisat2, hisat2_extractsplicesites, kallisto, rsem, rsem_make_transcript_fasta, salmon, sizes, star), 'sarek' (bwamem1, bwamem2, createsequencedictionary, dragmap, faidx, intervals, msisensorpro, snapaligner, tabix), 'null' (no tools). Can be combined with --tools and --skip_tools.", - "pattern": "^((all|null|rnaseq|sarek)?,?)*(?500M bp), 11 for compact genomes (<300M bp). If not specified, calculated as log2(genome_size)/2-1, capped at 14. Overrides per-genome values from the input datasheet; falls back to STAR defaults when neither is set.", "minimum": 1, - "maximum": 14 + "maximum": 14, + "errorMessage": "STAR genomeSAindexNbases must be an integer between 1 and 14" }, "hisat2_build_memory": { "type": "string", "description": "Memory threshold for HISAT2 index building. When available process memory meets or exceeds this value, splice sites and exons are used to build a splice-aware index.", "fa_icon": "fas fa-memory", "default": "200.GB", - "pattern": "^[0-9]+\\.?[0-9]*\\.?[GMK]B$" + "pattern": "^[0-9]+\\.?[0-9]*\\.?[GMK]B$", + "errorMessage": "HISAT2 build memory must be a memory value such as '200.GB', '3.GB' or '512MB'" }, "hisat2_skip_splice_sites": { "type": "boolean", diff --git a/subworkflows/local/utils_references/schema_references.json b/subworkflows/local/utils_references/schema_references.json index 166dee9d..87809778 100644 --- a/subworkflows/local/utils_references/schema_references.json +++ b/subworkflows/local/utils_references/schema_references.json @@ -43,31 +43,31 @@ "meta": ["ascat_alleles"], "type": "string", "pattern": "^\\S+$", - "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"],