docs: Add host removal to schema

dalmolingroup · Mar 24, 2024 · e2d74d3 · e2d74d3
1 parent 6bc6f2c
commit e2d74d3
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Showing 2 changed files with 25 additions and 5 deletions.
diff --git a/docs/params.md b/docs/params.md
@@ -23,6 +23,7 @@ Choose to skip pipeline steps
 | `skip_classification` | Skip taxonomic classification | `boolean` |  |  |  |
 | `skip_alignment` | Skip alignment | `boolean` |  |  |  |
 | `skip_functional` | Skip functional annotation | `boolean` |  |  |  |
+| `skip_host_removal` | Skip host removal | `boolean` |  |  |  |
 
 ## Decontamination
 

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",
@@ -66,6 +69,11 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-database",
                     "description": "Skip functional annotation"
+                },
+                "skip_host_removal": {
+                    "type": "boolean",
+                    "description": "Skip host removal",
+                    "fa_icon": "fab fa-ioxhost"
                 }
             },
             "fa_icon": "fas fa-angle-double-right"
@@ -136,7 +144,9 @@
                     "description": "Run Kraken2 classifier"
                 }
             },
-            "required": ["kaiju_db"],
+            "required": [
+                "kaiju_db"
+            ],
             "fa_icon": "fab fa-pagelines"
         },
         "functional": {
@@ -170,7 +180,9 @@
                     "description": "Maximum evalue of a match to be used for annotation"
                 }
             },
-            "required": ["id_mapping"],
+            "required": [
+                "id_mapping"
+            ],
             "fa_icon": "fas fa-gavel"
         },
         "assembly": {
@@ -278,7 +290,14 @@
                     "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": {
@@ -394,4 +413,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}