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fellen31 committed Nov 22, 2024
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

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## 0.4.0 - [2024-11-22]

### `Added`
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> Version has been removed if new version information isn't present.
## 0.3.2 - [2024-09-20]
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## v0.3.2 - [2024-09-20]
>>>>>>> master
### `Fixed`

- [#396](https://github.com/genomic-medicine-sweden/nallo/pull/396) - Fixed the release test profile not working, by pinning the testdata used [#395](https://github.com/genomic-medicine-sweden/nallo/issues/395)

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## 0.3.1 - [2024-09-11]
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## v0.3.1 - [2024-09-11]
>>>>>>> master
### `Fixed`

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141 changes: 141 additions & 0 deletions nextflow_schema.json
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}
},
"required": ["preset"]
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},
"file_inputs": {
"title": "File inputs",
"type": "object",
"description": "The different files that are required. Some are only required by certain workflows, see the usage documentation.",
"default": "",
"fa_icon": "fas fa-copy",
"properties": {
"cadd_prescored": {
"type": "string",
"exists": true,
"format": "directory-path",
"fa_icon": "fas fa-file",
"description": "Path to a directory containing prescored indels for CADD.",
"help_text": "This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
},
"cadd_resources": {
"type": "string",
"exists": true,
"format": "directory-path",
"fa_icon": "fas fa-file",
"description": "Path to a directory containing CADD annotations.",
"help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
},
"par_regions": {
"type": "string",
"description": "Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant",
"format": "file-path",
"exists": true
},
"tandem_repeats": {
"type": "string",
"format": "file-path",
"description": "A tandem repeat BED file for sniffles",
"pattern": "^\\S+\\.bed$",
"exists": true
},
"trgt_repeats": {
"type": "string",
"description": "A BED file with repeats to be genotyped with TRGT",
"format": "file-path",
"exists": true
},
"snp_db": {
"type": "string",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"mimetype": "text/csv",
"schema": "/assets/schema_snpdb.json",
"description": "A csv file with echtvar databases to annotate SNVs with",
"exists": true
},
"variant_catalog": {
"type": "string",
"description": "A variant catalog json-file for stranger",
"format": "file-path",
"exists": true
},
"variant_consequences_snv": {
"type": "string",
"description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs.",
"help_text": "For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
"fa_icon": "fas fa-file-csv"
},
"vep_cache": {
"type": "string",
"description": "A path to the VEP cache location",
"format": "path",
"exists": true
},
"bed": {
"type": "string",
"pattern": "^\\S+\\.bed$",
"format": "file-path",
"description": "A BED file with regions of interest, used to limit short variant calling.",
"exists": true
},
"hificnv_xy": {
"type": "string",
"format": "file-path",
"description": "A BED file containing expected copy number regions for XY samples.",
"exists": true
},
"hificnv_xx": {
"type": "string",
"format": "file-path",
"description": "A BED file containing expected copy number regions for XX samples.",
"exists": true
},
"hificnv_exclude": {
"type": "string",
"format": "file-path",
"description": "A BED file specifying regions to exclude with HiFiCNV, such as centromeres.",
"exists": true
},
"reduced_penetrance": {
"type": "string",
"exists": true,
"format": "path",
"fa_icon": "fas fa-file-csv",
"description": "A file with gene ids that have reduced penetrance. For use with genmod."
},
"score_config_snv": {
"type": "string",
"exists": true,
"format": "path",
"fa_icon": "fas fa-file",
"description": "A SNV rank model config file for genmod."
},
"somalier_sites": {
"type": "string",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"description": "A VCF of known polymorphic sites for somalier",
"format": "file-path",
"exists": true
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warning."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/",
"hidden": true
}
}
>>>>>>> master
}
},
"allOf": [
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