update nextflow schema

sanger-tol · Sep 17, 2023 · d4b93da · d4b93da
1 parent 1023126
commit d4b93da
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Showing 3 changed files with 36 additions and 8 deletions.
diff --git a/assets/test/mMelMel3.1.buscogenes.dmnd b/assets/test/mMelMel3.1.buscogenes.dmnd
diff --git a/nextflow.config b/nextflow.config
@@ -178,7 +178,7 @@ profiles {
     }
     cleanup   { cleanup = true                        }
     test      { includeConfig 'conf/test.config'      }
-    test_raw  { includeConfig 'conf/test_raw.config   }
+    test_raw  { includeConfig 'conf/test_raw.config'  }
     test_full { includeConfig 'conf/test_full.config' }
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "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",
@@ -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"
         }
     ]
-}
+}