Merge branch 'schema_split' into 'dev'

Seperated out the params into logical sections

See merge request epi2melabs/workflow-containers/wf-isoforms!40

environment.yaml

@@ -6,7 +6,7 @@ channels:
     - defaults
 dependencies:
     - python==3.8.*
-    - aplanat >=0.5.0
+    - aplanat >=0.6.2
     - epi2melabs
     - minimap2 ==2.24
     - samtools ==1.14

nextflow_schema.json

@@ -37,24 +37,29 @@
                     "description": "Use additional heuristics to identify barcodes from file paths.",
                     "help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
                 },
-                "plot_gffcmp_stats": {
-                    "type": "boolean",
-                    "description": "Create a pdf of plots from showing gffcompare results"
-                },
-                "gffcompare_opts": {
-                    "type": "string",
-                    "description": "Extra options for gffcompare -r",
-                    "default": " -R "
-                },
                 "ref_genome": {
                     "type": "string",
                     "format": "file-path",
-                    "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
+                    "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow"
                 },
                 "ref_annotation": {
                     "type": "string",
                     "format": "file-path",
                     "description": "A reference annotation of gff format"
+                }
+            },
+            "required": [
+                "fastq"
+            ]
+        },
+        "global_options": {
+            "title":  "Global options",
+            "type":  "object",
+            "description":  "Options for both sub-workflows",
+            "properties": {
+                "threads": {
+                    "type": "integer",
+                    "default": 4
                 },
                 "use_pychopper": {
                     "type": "boolean",
@@ -66,9 +71,40 @@
                     "description": "Extra pychopper opts",
                     "default": "-m edlib"
                 },
-                "threads": {
+                "bundle_min_reads": {
                     "type": "integer",
-                    "default": 8
+                    "description": "Minimum size of bam bundle for parallel processing."
+                },
+                "stringtie_opts": {
+                    "type": "string",
+                    "description": "Extra options for stringtie transcript assembly.",
+                    "default": " --conservative "
+                },
+                "transcript_table_cov_thresh": {
+                    "type": "integer",
+                    "description": "Minimum coverage for a transcript to appear in the report table",
+                    "default": 50
+                },
+                "denovo": {
+                    "type": "boolean",
+                    "description": "Use denovo transcript assembly rather than reference guided",
+                    "default": false
+                }
+            }
+        },
+            "reference_wf_options": {
+                "title": "Options for reference-based workflow",
+                "type": "object",
+                "description": "Parameters that are used solely for the referenc-guided workflow",
+                "properties": {
+                    "plot_gffcmp_stats": {
+                        "type": "boolean",
+                        "description": "Create a pdf of plots from showing gffcompare results"
+                    },
+                    "gffcompare_opts": {
+                        "type": "string",
+                        "description": "Extra options for gffcompare -r",
+                        "default": " -R "
                     },
                     "minimap_index_opts": {
                         "type": "string",
@@ -94,34 +130,15 @@
                         "type": "integer",
                         "description": "Max poly(A) region allowed with poly_context-sized end regions.",
                         "default": 8
+                    }
+                    
+                }
             },
-                "bundle_min_reads": {
+            "denovo_wf_options": {
-                    "type": "integer",
+                "title": "Options for de novo-based workflow",
-                    "description": "Minimum size of bam bundle for parallel processing."
+                "type": "object",
-                },
+                "description": "Parameters that are used solely for the de novo workflow",
-                "use_guide_annotation": {
+                "properties": {
-                    "type": "boolean",
-                    "description": "Use reference annotation in stringtie transcript assembly.",
-                    "default": "true"
-                },
-                "stringtie_opts": {
-                    "type": "string",
-                    "description": "Extra options for stringtie transcript assembly.",
-                    "default": " --conservative "
-                },
-                "disable_ping": {
-                    "type": "boolean"
-                },
-                "transcript_table_cov_thresh": {
-                    "type": "integer",
-                    "description": "Minimum coverage for a transcript to appear in the report table",
-                    "default": 50
-                },
-                "denovo": {
-                    "type": "boolean",
-                    "description": "Use denovo transcript assembly rather than reference guided",
-                    "default": false
-                },
                     "batch_size": {
                         "type": "integer",
                         "description": "Maximum sequences per input batch (-1 means no limit)",
@@ -197,10 +214,7 @@
                         "description": "Minimum probability for i consecutive minimizers to be different between read and representative",
                         "default": 0.2
                     }
-            },
+            }
-            "required": [
-                "fastq"
-            ]
         },
         "meta_data": {
             "title": "Meta Data",
@@ -212,6 +226,12 @@
                     "type": "string",
                     "default": "report",
                     "description": "Output report filename suffix."
+                },
+                "disable_ping": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Enable to prevent sending a workflow ping."
+
                 }
             }
         },
@@ -231,10 +251,20 @@
             }
         }
     },
+   
     "allOf": [
         {
             "$ref": "#/definitions/basic_input_output_options"
         },
+        {
+            "$ref": "#/definitions/global_options"
+        },
+        {
+            "$ref": "#/definitions/reference_wf_options"
+        },
+        {
+            "$ref": "#/definitions/denovo_wf_options"
+        },
         {
             "$ref": "#/definitions/meta_data"
         },
@@ -253,7 +283,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.1.0",
+            "default": "v0.1.1",
             "hidden": true
         },
         "monochrome_logs": {