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"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", @@ -22,6 +25,10 @@ "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.", "fa_icon": "fas fa-file-csv" }, + "align": { + "type": "boolean", + "description": "Boolean to turn on optional alignment before running the rest of the pipeline." + }, "yaml": { "type": "string", "format": "file-path", @@ -54,7 +61,11 @@ "type": "object", "fa_icon": "fas fa-dna", "description": "Reference genome related files and options required for the workflow.", - "required": ["taxon", "accession", "fasta"], + "required": [ + "taxon", + "accession", + "fasta" + ], "properties": { "taxon": { "type": "string", @@ -79,7 +90,10 @@ "type": "object", "fa_icon": "fas fa-database", "description": "Define the location and parameters to work with databases.", - "required": ["uniprot", "taxdump"], + "required": [ + "uniprot", + "taxdump" + ], "properties": { "taxa_file": { "type": "string", @@ -101,7 +115,15 @@ }, "blastp_outext": { "type": "string", - "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"], + "enum": [ + "blast", + "xml", + "txt", + "daa", + "sam", + "tsv", + "paf" + ], "description": "Extension (file format) of the output file from Diamond BLAST.", "fa_icon": "fas fa-file-circle-question", "default": "txt" @@ -229,7 +251,14 @@ "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": { @@ -328,4 +357,4 @@ "$ref": "#/definitions/generic_options" } ] -} +} \ No newline at end of file