Fixed up parameters

phac-nml · Jan 25, 2024 · ba17901 · ba17901
1 parent fa5464b
commit ba17901
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Showing 2 changed files with 8 additions and 30 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -11,9 +11,6 @@ params {
 
     // Input options
     input                      = null
-    project_name               = 'assembly'
-    assembler                  = 'stub'
-    random_seed                = 1
 
     // Boilerplate options
     outdir                     = null
@@ -198,7 +195,7 @@ manifest {
     description     = """IRIDA Next pipeline for fetching data from NCBI"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.1.0.dev'
+    version         = '1.0.0.dev'
     doi             = ''
     defaultBranch   = 'main'
 }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -27,35 +27,16 @@
                     "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"
-                },
-                "project_name": {
-                    "type": "string",
-                    "default": "assembly",
-                    "pattern": "^\\S+$",
-                    "description": "The name of the project.",
-                    "fa_icon": "fas fa-tag"
-                },
-                "assembler": {
-                    "type": "string",
-                    "default": "stub",
-                    "fa_icon": "fas fa-desktop",
-                    "description": "The sequence assembler to use for sequence assembly.",
-                    "enum": ["default", "stub", "experimental"]
-                },
-                "random_seed": {
-                    "type": "integer",
-                    "default": 1,
-                    "fa_icon": "fas fa-dice-six",
-                    "description": "The random seed to use for sequence assembly.",
-                    "minimum": 1
+                    "fa_icon": "fas fa-folder-open",
+                    "hidden": true
                 },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
-                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+                    "hidden": true
                 }
             }
         },
@@ -102,15 +83,15 @@
                 "max_cpus": {
                     "type": "integer",
                     "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
+                    "default": 4,
                     "fa_icon": "fas fa-microchip",
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                 },
                 "max_memory": {
                     "type": "string",
                     "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
+                    "default": "2.GB",
                     "fa_icon": "fas fa-memory",
                     "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                     "hidden": true,
@@ -119,7 +100,7 @@
                 "max_time": {
                     "type": "string",
                     "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
+                    "default": "1.h",
                     "fa_icon": "far fa-clock",
                     "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                     "hidden": true,