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FIX: Remove default null in schema #1119

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merged 3 commits into from
Jun 20, 2023
Merged

FIX: Remove default null in schema #1119

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5acab8e
remove default = null from schema
maxulysse Jun 19, 2023
0c1770a
add help_text for input_output_options
maxulysse Jun 19, 2023
6e638e4
update CHANGELOG
maxulysse Jun 19, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,9 +10,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

- [#1112](https://github.com/nf-core/sarek/pull/1112) - Back to dev
- [#1119](https://github.com/nf-core/sarek/pull/1119) - Added `help_text` for `input_output_options` group in schema

### Changed

- [#1119](https://github.com/nf-core/sarek/pull/1119) - Remove `null` by default in schema

### Fixed

## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah
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26 changes: 12 additions & 14 deletions nextflow_schema.json
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Expand Up @@ -10,8 +10,19 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"help_text": "Specify input samplesheet, step and output folder.",
"required": ["step", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory.",
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Are the two linebreaks here intended or should it just be one linebreak?

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I actually just moved that part around, so never notice the line breaks, so I'd say that yeah, they are intended

"fa_icon": "fas fa-file-csv"
},
"step": {
"type": "string",
"default": "mapping",
Expand All @@ -27,24 +38,13 @@
"annotate"
]
},
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory.",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
}
},
"help_text": ""
}
},
"main_options": {
"title": "Main options",
Expand Down Expand Up @@ -345,7 +345,6 @@
},
"cnvkit_reference": {
"type": "string",
"default": null,
"fa_icon": "fas fa-file",
"help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch",
"description": "Copy-number reference for CNVkit",
Expand Down Expand Up @@ -528,7 +527,6 @@
"ascat_genome": {
"type": "string",
"fa_icon": "fa-solid fa-text",
"default": null,
"description": "ASCAT genome.",
"help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nMust be set to run ASCAT, either hg19 or hg38. If you use AWS iGenomes, this has already been set for you appropriately.",
"enum": ["None", "hg19", "hg38"],
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