transfer parameter definitions from deepmutscan.nf to nextflow.config

nextflow.config

@@ -27,11 +27,13 @@ params {
 
     min_counts			= 3
     mutagenesis_type		= 'nnk'
-    fitness			= false
-    dimsum			= false
     run_seqdepth		= false
     reading_frame		= null
     custom_codon_library	= '/NULL'
+    sliding_window_size		= 10
+    aimed_cov			= 100
+    fitness			= false
+    dimsum			= false
 
     // Boilerplate options
     outdir                       = null

nextflow_schema.json

@@ -48,24 +48,34 @@
                 },
                 "min_counts": {
                     "type": "integer",
-                    "description": "Minimum number of variant observations required.",
+                    "description": "minimum counts for variant to be recognized. All variants below min_counts will be set to 0",
                     "minimum": 1,
                     "default": 3
                 },
+		"sliding_window_size": {
+                    "type": "integer",
+                    "description": "To flatten graphs in plots (e.g. GLOBAL_POS_BIASES_COUNTS function)",
+                    "default": 10
+                },
+		"aimed_cov": {
+                    "type": "integer",
+                    "description": "aimed coverage (assuming equal spread) to visualize threshold in plots",
+                    "default": 100
+                },
                 "mutagenesis_type": {
                     "type": "string",
-                    "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'",
+                    "description": "Type of mutagenic primers. Choose from nnk, nns, max_diff_to_wt, custom. When using 'custom', also provide the parameter 'custom_codon_library'. Default library is set to nnk",
                     "default": "nnk"
                 },
                 "custom_codon_library": {
                     "type": "string",
                     "format": "file-path",
-                    "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is 'custom'."
+                    "description": "Path to a comma-separated .txt file listing custom codons (e.g., 'AAA,AAC,AAG,...'). Required when mutagenesis_type is set to 'custom'."
                 },
                 "dimsum": {
                     "type": "boolean",
                     "default": false,
-                    "description": "Enable DiMSum execution."
+                    "description": "Run DiMSum for fitness/functionality scores from grwoth-based selection input & output samples"
                 },
                 "fitness": {
                     "type": "boolean",
@@ -75,7 +85,7 @@
                 "run_seqdepth": {
                     "type": "boolean",
                     "default": false,
-                    "description": "Whether to run the SeqDepth simulation module. This is computationally intensive and optional."
+                    "description": "Whether to run the SeqDepth simulation module, to check on the sequencing depth. This is computationally intensive and optional."
                 }
             }
         },

workflows/deepmutscan.nf

@@ -38,17 +38,6 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_deep
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Params defaults
-params.min_counts 	= 3                                     // minimum counts for variant to be recognized. All variants<min_counts will be set to 0
-params.mutagenesis_type = 'nnk'                      		// default library is set to nnk
-params.custom_codon_library = '/NULL'            		// when mutagenesis_type is set to >>custom<< this variable has to be path to .txt with custom library
-params.sliding_window_size = 10 				// sliding window size to flatten graphs in plots (e.g. GLOBAL_POS_BIASES_COUNTS function)
-params.aimed_cov 	= 100                                  	// aimed coverage (assuming equal spread) to visualize threshold in plots
-params.run_seqdepth 	= false         			// creating seqdepth simulation plot, is computationally quite heavy. per default disabled.
-params.fitness      	= false 				// run basic fitness calculation from selection input & output samples
-params.dimsum       	= false					// run DiMSum for fitness/functionality scores from selection input & output samples
-
-
 // Define fasta file as channel (e.g. for BWA index)
 Channel
     .fromPath(params.fasta, checkIfExists: true)