Update README.md, nextflow_schema.json

README.md

@@ -44,6 +44,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
    - [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)
    - [Kaiju](https://kaiju.binf.ku.dk/)
    - [mOTUs](https://motu-tool.org/)
+   - [MetaMaps](https://github.com/DiltheyLab/MetaMaps)
 4. Perform optional post-processing with:
    - [bracken](https://ccb.jhu.edu/software/bracken/)
 5. Standardises output tables

modules.json

@@ -50,6 +50,9 @@
             },
             "untar": {
                 "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
+            },
+            "kaiju/kaiju": {
+                "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
             }
         }
     }

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",
@@ -173,7 +176,14 @@
                     "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": {
@@ -294,7 +304,10 @@
         "shortread_clipmerge_tool": {
             "type": "string",
             "default": "fastp",
-            "enum": ["fastp", "adapterremoval"]
+            "enum": [
+                "fastp",
+                "adapterremoval"
+            ]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
@@ -335,7 +348,10 @@
         "shortread_complexityfilter_prinseqplusplus_mode": {
             "type": "string",
             "default": "entropy",
-            "enum": ["entropy", "dust"]
+            "enum": [
+                "entropy",
+                "dust"
+            ]
         },
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",
@@ -364,11 +380,15 @@
         },
         "shortread_hostremoval_reference": {
             "type": "string",
-            "default": null
+            "default": "None"
         },
         "shortread_hostremoval_index": {
             "type": "string",
-            "default": null
+            "default": "None"
+        },
+        "run_kaiju": {
+            "type": "string",
+            "default": "false"
         }
     }
-}
+}