Fix conflict

nextflow_schema.json

@@ -10,7 +10,11 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-      "required": ["input", "databases", "outdir"],
+            "required": [
+                "input",
+                "databases",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -80,7 +84,10 @@
                 "shortread_qc_tool": {
                     "type": "string",
                     "default": "fastp",
-          "enum": ["fastp", "adapterremoval"],
+                    "enum": [
+                        "fastp",
+                        "adapterremoval"
+                    ],
                     "fa_icon": "fas fa-tools",
                     "description": "Specify which tool to use for short-read QC"
                 },
@@ -139,7 +146,11 @@
                 "shortread_complexityfilter_tool": {
                     "type": "string",
                     "default": "bbduk",
-          "enum": ["bbduk", "prinseqplusplus", "fastp"],
+                    "enum": [
+                        "bbduk",
+                        "prinseqplusplus",
+                        "fastp"
+                    ],
                     "fa_icon": "fas fa-hammer",
                     "description": "Specify which tool to use for complexity filtering"
                 },
@@ -173,7 +184,10 @@
                 "shortread_complexityfilter_prinseqplusplus_mode": {
                     "type": "string",
                     "default": "entropy",
-          "enum": ["entropy", "dust"],
+                    "enum": [
+                        "entropy",
+                        "dust"
+                    ],
                     "fa_icon": "fas fa-check-square",
                     "description": "Specify the complexity filter mode for PRINSEQ++"
                 },
@@ -347,7 +361,15 @@
                 "diamond_output_format": {
                     "type": "string",
                     "default": "tsv",
-          "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
+                    "enum": [
+                        "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`"
@@ -366,7 +388,14 @@
                 "kaiju_taxon_rank": {
                     "type": "string",
                     "default": "species",
-          "enum": ["phylum", "class", "order", "family", "genus", "species"],
+                    "enum": [
+                        "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`"
@@ -432,6 +461,18 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
+                },
+                "save_mgc_counts": {
+                    "type": "boolean",
+                    "description": "Save the mgc reads count for mOTUs."
+                },
+                "save_read_counts": {
+                    "type": "boolean",
+                    "description": "Print mOTUs result as counts instead of relative abundances."
+                },
+                "save_ncbi_id": {
+                    "type": "boolean",
+                    "description": "Print NCBI taxonomic id for mOTUs."
                 }
             },
             "fa_icon": "fas fa-align-center"
@@ -607,7 +648,10 @@
                 "preprocessing_qc_tool": {
                     "type": "string",
                     "default": "fastqc",
-          "enum": ["fastqc", "falco"],
+                    "enum": [
+                        "fastqc",
+                        "falco"
+                    ],
                     "help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
                     "description": "Specify the tool used for quality control of raw sequencing reads"
                 },
@@ -738,19 +782,5 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         }
-  ],
+    ]
-  "properties": {
-    "save_mgc_counts": {
-      "type": "boolean",
-      "description": "Save the mgc reads count for mOTUs."
-    },
-    "save_ncbi_id": {
-      "type": "boolean",
-      "description": "Print NCBI taxonomic id for mOTUs."
-    },
-    "save_read_counts": {
-      "type": "boolean",
-      "description": "Print mOTUs result as counts instead of relative abundances."
-    }
-  }
 }