diff --git a/nextflow_schema.json b/nextflow_schema.json index 56cdc6edaf..0a23d33f62 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "step", - "outdir" - ], + "required": ["step", "outdir"], "properties": { "step": { "type": "string", @@ -190,11 +187,7 @@ "type": "string", "default": "bwa-mem", "fa_icon": "fas fa-puzzle-piece", - "enum": [ - "bwa-mem", - "bwa-mem2", - "dragmap" - ], + "enum": ["bwa-mem", "bwa-mem2", "dragmap"], "description": "Specify aligner to be used to map reads to reference genome.", "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> `Sarek` will build them automatically if not provided.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes.", "hidden": true @@ -428,11 +421,7 @@ "type": "string", "default": "vcf", "description": "VEP output-file format.", - "enum": [ - "json", - "tab", - "vcf" - ], + "enum": ["json", "tab", "vcf"], "help_text": "Sets the format of the output-file from VEP. Available formats: json, tab and vcf.", "fa_icon": "fas fa-table" } @@ -773,14 +762,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email": {