finished all inputs testing, getting closer to master release, few more tasks to get to

Author: number-25

.nf-core.yml

@@ -41,7 +41,7 @@ lint:
   #    - manifest.name
   #    - manifest.homePage
   nf_test_content: False
-nf_core_version: 3.3.2
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   prefix: number-25

conf/test_full.config

@@ -18,10 +18,10 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data
-    input                           = "test/samplesheets/samplesheet_test_local.csv"
-    //input                           = "test/samplesheets/samplesheet_test_local_bam.csv"
+    //input                           = "test/samplesheets/samplesheet_test_local.csv"
+    input                           = "test/samplesheets/samplesheet_test_local_bam.csv"
     sequencing_type                 = "ont-drna" // sequencing molecule [ont-drna OR ont-cdna]
-    bam_input                       = false
+    bam_input                       = true
     transcriptome_mapping           = false
     // Genome references
     // These channel names have to match those in the full workflow also

nextflow_schema.json

@@ -78,7 +78,8 @@
                     "type": "string",
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "fa_icon": "fas fa-folder-open"
+                    "fa_icon": "fas fa-folder-open",
+                    "default": "outputs"
                 },
                 "help": {
                     "type": "boolean",
@@ -257,7 +258,8 @@
                 },
                 "skip_flair_correct": {
                     "type": "boolean",
-                    "description": "Skip FLAIR correct module."
+                    "description": "Skip FLAIR correct module.",
+                    "default": true
                 },
                 "extra_flair_correct_options": {
                     "type": "string",
@@ -273,7 +275,6 @@
                 },
                 "skip_bambu": {
                     "type": "boolean",
-                    "default": true,
                     "description": "Skip bambu transcript reconstruction."
                 },
                 "extra_bambu_options": {
@@ -290,7 +291,6 @@
                 },
                 "skip_isoquant": {
                     "type": "boolean",
-                    "default": true,
                     "description": "Skip IsoQuant transcript reconstruction."
                 },
                 "skip_isoquant_correction": {