update schema

Ferlab-Ste-Justine · Jan 28, 2025 · 91f3ea3 · 91f3ea3
1 parent f65560f
commit 91f3ea3
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Showing 2 changed files with 35 additions and 8 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -23,10 +23,11 @@ params {
     dbsnpFile = null
     dbsnpFileIndex = null
     tools = ""
-    vep_cache = null
+    vep_cache = null // Null if download cache = true
     vep_cache_version = null
     vep_genome = null
     download_cache = false
+    outdir_cache     = null // If not declared, cache will be downloaded in outputdir/cache/
     exomiser_genome  = null
     exomiser_data_dir = null
     exomiser_data_version = null
@@ -45,14 +46,16 @@ params {
     exclude_mnps = true
     TSfilterSNP = '99'
     TSfilterINDEL = '99'
-    hardFilters = [[name: 'QD2', expression: 'QD < 2.0'],
+    hardFilters = [
+        [name: 'QD2', expression: 'QD < 2.0'],
         [name: 'QD1', expression: 'QD < 1.0'],
         [name: 'QUAL30', expression: 'QUAL < 30.0'],
         [name: 'SOR3', expression: 'SOR > 3.0'],
         [name: 'FS60', expression: 'FS > 60.0'],
         [name: 'MQ40', expression: 'MQ < 40.0'],
         [name: 'MQRankSum-12.5', expression: 'MQRankSum < -12.5'],
-        [name: 'ReadPosRankSum-8', expression: 'ReadPosRankSum < -8.0']]
+        [name: 'ReadPosRankSum-8', expression: 'ReadPosRankSum < -8.0']
+    ]
 
 
     allow_old_gatk_data = false
@@ -66,7 +69,6 @@ params {
 
     // Boilerplate options
     outdir                       = null
-    outdir_cache                 = null
     publish_all                  = false
     publish_dir_mode             = 'copy'
     monochrome_logs              = false
@@ -94,7 +96,7 @@ params {
 includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
-try {
+try { 
     includeConfig "${params.custom_config_base}/nfcore_custom.config"
 } catch (Exception e) {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
@@ -272,7 +274,7 @@ process {
 		disk	=	{ check_max( 30.GB	* task.attempt, 'disk'		)	}
 		time	=	{ check_max( 10.h	* task.attempt, 'time'		)	}
 	}
-  	withName: 'GATK4_VARIANTFILTRATION' {
+    withName: 'GATK4_VARIANTFILTRATION' {
 		errorStrategy = 'retry'
 		maxRetries = 2
 		cpus	=	{ check_max( 2		* task.attempt, 'cpus'		) 	}
@@ -288,7 +290,15 @@ process {
 		disk	=	{ check_max( 30.GB	* task.attempt, 'disk'		)	}
 		time	=	{ check_max( 10.h	* task.attempt, 'time'		)	}
 	}
-	withName: 'ENSEMBLVEP_VEP|ENSEMBLVEP_DOWNLOAD' {
+	withName: 'ENSEMBLVEP_DOWNLOAD' {
+		errorStrategy = 'retry'
+		maxRetries = 2
+		cpus	=	{ check_max( 4 		* task.attempt, 'cpus'		)	}
+		memory	=	{ check_max( 36.GB	* task.attempt, 'memory'	)	}
+		disk	=	{ check_max( 140.GB	* task.attempt, 'disk'		)	}
+		time	=	{ check_max( 8.h 	* task.attempt, 'time'		)	}
+	}
+	withName: 'ENSEMBLVEP_VEP' {
 		errorStrategy = 'retry'
 		maxRetries = 2
 		cpus	=	{ check_max( 4 		* task.attempt, 'cpus'		)	}

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -281,9 +281,26 @@
                 },
                 "hardFilters": {
                     "type": "array",
+                    "items": {
+                        "type": "object",
+                        "properties": {
+                            "name": { "type": "string" },
+                            "expression": { "type": "string" }
+                        },
+                        "required": ["name", "expression"]
+                    },
                     "description": "Parameters for Hard-Filtering",
                     "help_text": "Parameters for Hard-Filtering. Must be an array containing each desired filter. Each filter must be formatted with the desired name and expression, for example\\n[[name: 'QD1', expression: 'QD < 1.0'],[name: 'QD2', expression: 'QD < 2.0]]",
-                    "default": "[[name:'QD2', expression:'QD < 2.0'], [name:'QD1', expression:'QD < 1.0'], [name:'QUAL30', expression:'QUAL < 30.0'], [name:'SOR3', expression:'SOR > 3.0'], [name:'FS60', expression:'FS > 60.0'], [name:'MQ40', expression:'MQ < 40.0'], [name:'MQRankSum-12.5', expression:'MQRankSum < -12.5'], [name:'ReadPosRankSum-8', expression:'ReadPosRankSum < -8.0']]"
+                    "default": [
+                        { "name": "QD1", "expression": "QD < 1.0" },
+                        { "name": "QD2", "expression": "QD < 2.0" },
+                        { "name": "QUAL30", "expression": "QUAL < 30.0" },
+                        { "name": "SOR3", "expression": "SOR > 3.0" },
+                        { "name": "FS60", "expression": "FS > 60.0" },
+                        { "name": "MQ40", "expression": "MQ < 40.0" },
+                        { "name": "MQRankSum-12.5", "expression": "MQRankSum < -12.5" },
+                        { "name": "ReadPosRankSum-8", "expression": "ReadPosRankSum < -8.0" }
+                    ]
                 },
                 "allow_old_gatk_data": {
                     "type": "boolean",