Prettier

docs/usage.md

@@ -165,9 +165,11 @@ work                # Directory containing the nextflow working files
 .nextflow_log       # Log file from Nextflow
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
+
 ### Sequencing quality control
 
 nf-core taxprofiler offers [`Falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+
 ### Preprocessing Steps
 
 nf-core/taxprofiler offers four main preprocessing steps

nextflow_schema.json

@@ -10,11 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
+            "required": ["input", "outdir", "databases"],
-                "input",
-                "outdir",
-                "databases"
-            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -84,10 +80,7 @@
                 "shortread_qc_tool": {
                     "type": "string",
                     "default": "fastp",
-                    "enum": [
+                    "enum": ["fastp", "adapterremoval"],
-                        "fastp",
-                        "adapterremoval"
-                    ],
                     "fa_icon": "fas fa-tools",
                     "description": "Specify which tool to use for short-read QC"
                 },
@@ -140,11 +133,7 @@
                 "shortread_complexityfilter_tool": {
                     "type": "string",
                     "default": "bbduk",
-                    "enum": [
+                    "enum": ["bbduk", "prinseqplusplus", "fastp"],
-                        "bbduk",
-                        "prinseqplusplus",
-                        "fastp"
-                    ],
                     "fa_icon": "fas fa-hammer",
                     "description": "Specify which tool to use for complexity filtering"
                 },
@@ -178,10 +167,7 @@
                 "shortread_complexityfilter_prinseqplusplus_mode": {
                     "type": "string",
                     "default": "entropy",
-                    "enum": [
+                    "enum": ["entropy", "dust"],
-                        "entropy",
-                        "dust"
-                    ],
                     "fa_icon": "fas fa-check-square",
                     "description": "Specify the complexity filter mode for PRINSEQ++"
                 },
@@ -355,15 +341,7 @@
                 "diamond_output_format": {
                     "type": "string",
                     "default": "tsv",
-                    "enum": [
+                    "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
-                        "blast",
-                        "xml",
-                        "txt",
-                        "daa",
-                        "sam",
-                        "tsv",
-                        "paf"
-                    ],
                     "fa_icon": "fas fa-file",
                     "description": "Specify output format from DIAMOND profiling.",
                     "help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
@@ -382,14 +360,7 @@
                 "kaiju_taxon_rank": {
                     "type": "string",
                     "default": "species",
-                    "enum": [
+                    "enum": ["phylum", "class", "order", "family", "genus", "species"],
-                        "phylum",
-                        "class",
-                        "order",
-                        "family",
-                        "genus",
-                        "species"
-                    ],
                     "fa_icon": "fas fa-tag",
                     "description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
                     "help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
@@ -584,14 +555,7 @@
                     "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": [
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
                     "hidden": true
                 },
                 "email_on_fail": {