PR revisions

conf/modules.config

@@ -72,7 +72,8 @@ process {
     }
 
     withName: ENSEMBLVEP_DOWNLOAD {
-        container = 'quay.io/biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' // Trying with the conda container
+        // Using the conda container as the official one from esemblorg does not have the download_vep function used in nf-core. 
+        container = 'quay.io/biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' 
         ext.when  = { params.tools && (params.tools.split(',').contains('vep')) }
         ext.args  = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
         ext.prefix  = { "${params.vep_cache_version}_${params.vep_genome}" }

nextflow.config

@@ -23,11 +23,11 @@ params {
     dbsnpFile = null
     dbsnpFileIndex = null
     tools = ""
-    vep_cache = null // Null if download cache = true
+    vep_cache = null
     vep_cache_version = null
     vep_genome = null
     download_cache = false
-    outdir_cache     = null // If not declared, cache will be downloaded in outputdir/cache/
+    outdir_cache     = null
     exomiser_genome  = null
     exomiser_data_dir = null
     exomiser_data_version = null
@@ -96,7 +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")
@@ -274,7 +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'		) 	}
@@ -306,15 +306,15 @@ process {
 		disk	=	{ check_max( 80.GB	* task.attempt, 'disk'		)	}
 		time	=	{ check_max( 10.h 	* task.attempt, 'time'		)	}
 	}
-    withName: 'EXOMISER' {
+	withName: 'EXOMISER' {
         errorStrategy = 'retry'
 		maxRetries = 2
 		cpus	=	{ check_max( 6 		* task.attempt, 'cpus'		)	}
 		memory	=	{ check_max( 36.GB	* task.attempt, 'memory'	)	}
 		disk	=	{ check_max( 150.GB	* task.attempt, 'disk'		)	}
 		time	=	{ check_max( 10.h 	* task.attempt, 'time'		)	}
     }
-    withName: 'writemeta' {
+	withName: 'writemeta' {
         container = 'ubuntu:24.10'	
     }
 }