diff --git a/modules.json b/modules.json index b568d9c..ce1fbc5 100644 --- a/modules.json +++ b/modules.json @@ -80,4 +80,4 @@ } } } -} \ No newline at end of file +} diff --git a/nextflow_schema.json b/nextflow_schema.json index 257f5cb..1902e27 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": [ - "input", - "outdir" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -176,14 +173,7 @@ "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_on_fail": { @@ -304,10 +294,7 @@ "shortread_clipmerge_tool": { "type": "string", "default": "fastp", - "enum": [ - "fastp", - "adapterremoval" - ] + "enum": ["fastp", "adapterremoval"] }, "shortread_clipmerge_skipadaptertrim": { "type": "boolean" @@ -348,10 +335,7 @@ "shortread_complexityfilter_prinseqplusplus_mode": { "type": "string", "default": "entropy", - "enum": [ - "entropy", - "dust" - ] + "enum": ["entropy", "dust"] }, "shortread_complexityfilter_prinseqplusplus_dustscore": { "type": "number", @@ -404,14 +388,7 @@ "kaiju_taxon_name": { "type": "string", "default": "species", - "enum": [ - "phylum", - "class", - "order", - "family", - "genus", - "species" - ] + "enum": ["phylum", "class", "order", "family", "genus", "species"] }, "run_diamond": { "type": "boolean" @@ -419,15 +396,7 @@ "diamond_output_format": { "type": "string", "default": "tsv", - "enum": [ - "blast", - "xml", - "txt", - "daa", - "sam", - "tsv", - "paf" - ] + "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"] }, "longread_hostremoval_index": { "type": "string", @@ -450,4 +419,4 @@ "description": "Flag for publishing fastq files for reads that did not map to the host reference" } } -} \ No newline at end of file +}