Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix

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", "databases", "outdir"],
-                "input",
-                "databases",
-                "outdir"
-            ],
             "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"
                 },
@@ -146,11 +139,7 @@
                 "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"
                 },
@@ -184,10 +173,7 @@
                 "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++"
                 },
@@ -361,15 +347,7 @@
                 "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`"
@@ -388,14 +366,7 @@
                 "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`"
@@ -590,14 +561,7 @@
                     "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": {
@@ -753,7 +717,10 @@
     "properties": {
         "preprocessing_qc_tool": {
             "type": "string",
-            "default": "fastqc"
+            "default": "fastqc",
+            "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"
         }
     }
 }