edited config, added schema

grp-bork · Jun 10, 2024 · 5bd21a9 · 5bd21a9
1 parent 0ac2644
commit 5bd21a9
Show file tree

Hide file tree

Showing 2 changed files with 117 additions and 4 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -7,15 +7,41 @@ manifest {
 	version = "0.12.6"
 }
 
+process {
+	withName: prepare_fastqs {
+		executor = "local"
+		scratch = null
+		container = null
+	}
+    withLabel: kraken2 {
+        container = "registry.git.embl.de/schudoma/kraken2-docker:latest"
+    }
+    withLabel: bbduk {
+        container = "quay.io/biocontainers/bbmap:39.06--h92535d8_0"
+    }
+	withLabel: gffquant {
+		container = "ghcr.io/cschu/gff_quantifier:v2.16.5"
+	}
+}
+
 params {
+	input_dir = null
+
+    //output
+    output_dir = null
 
-}
+	database = null
 
-process {
-
+    run_preprocessing = true
+    remove_host = false
+    drop_orphans = false
+    qc_minlen = 45
+    qc_params_shotgun = "qtrim=rl trimq=3 maq=25 ktrim=r k=23 mink=11 hdist=1 ftm=5 entropy=0.5 entropywindow=50 entropyk=5 tpe tbo"
+    remove_host_kraken2_db = null
+    kraken2_min_hit_groups = 10
+
 }
 
-
 docker {
 	enabled = true
 }
diff --git a/nextflow.schema b/nextflow.schema
@@ -0,0 +1,87 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/grp-bork/nevermore_profiler/main/nextflow_schema.json",
+    "title": "nevermore_profiler pipeline parameters",
+    "description": "nevermore_profiler JSON schema",
+    "type": "object",
+    "definitions": {
+        "preprocessing": {
+            "title": "preprocessing",
+            "type": "object",
+            "description": "Preprocessing parameters",
+            "default": "",
+            "properties": {
+                "qc_minlen": {
+                    "type": "integer",
+                    "description": "Minimum read length to pass quality control",
+                    "default": 45
+                },
+                "qc_params_shotgun": {
+                    "type": "string",
+                    "description": "bbduk quality control parameters",
+                    "default": "qtrim=rl trimq=3 maq=25 ktrim=r k=23 mink=11 hdist=1 ftm=5 entropy=0.5 entropywindow=50 entropyk=5 tpe tbo"
+                },
+                "remove_host_kraken2_db": {
+                    "type": "boolean",
+                    "description": "Path to a kraken2 database"
+                }
+            },
+            "required": [
+                "qc_minlen",
+                "qc_params_shotgun",
+                "remove_host_kraken2_db"
+            ]
+        },
+        "required": {
+            "title": "Required",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "input_dir": {
+                    "type": "directory-path",
+                    "description": "Directory path to fastq files",
+                    "format": "directory-path"
+                },
+                "output_dir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "Path to output directory"
+                },
+                "database": {
+                    "type": "directory-path",
+                    "description": "Path to annotation database"
+                }
+            },
+            "required": [
+                "input_dir",
+                "output_dir",
+				"database"
+            ]
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/preprocessing"
+        },
+        {
+            "$ref": "#/definitions/required"
+        }
+    ],
+    "properties": {
+        "run_preprocessing": {
+            "type": "boolean",
+            "default": true
+        },
+        "remove_host": {
+            "type": "boolean"
+        },
+        "drop_orphans": {
+            "type": "boolean"
+        },
+        "kraken2_min_hit_groups": {
+            "type": "integer",
+            "default": 10
+        }
+    }
+}