Bugfix: Fixes issue with sending email report

assets/email_template.txt

@@ -1,9 +1,4 @@
 ----------------------------------------------------
-                                        ,--./,-.
-        ___     __   __   __   ___     /,-._.--~\\
-  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
-  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
-                                        `._,._,'
   mskilab-org/nf-jabba v${version}
 ----------------------------------------------------
 Run Name: $runName

conf/base.config

@@ -37,14 +37,14 @@ process {
         time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 8     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 48.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 12.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
         cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
         memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 24.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
@@ -97,14 +97,14 @@ process {
         memory          = { check_max( 12.GB * task.attempt, 'memory' ) }
     }
     withName: 'SVABA' {
-        cpus            = { check_max( 16 * task.attempt, 'cpus' ) }
+        cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
         memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
-        time            = { check_max( 72.h  * task.attempt, 'time'   ) }
+        time            = 120.h
     }
     withName: 'GRIDSS' {
-        cpus            = { check_max( 16 * task.attempt, 'cpus' ) }
+        cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
         memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
-        time            = { check_max( 72.h  * task.attempt, 'time'    ) }
+        time            = 120.h
     }
     withName: 'GRIDSS_SOMATIC' {
         cpus            = { check_max( 8 * task.attempt, 'cpus' ) }

modules/local/svaba/main.nf

@@ -1,7 +1,7 @@
 
 process SVABA {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "bioconda::svaba=1.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

nextflow.config

@@ -186,8 +186,8 @@ params {
 	// Config options
 	config_profile_name        = null
 	config_profile_description = null
-	//custom_config_version      = 'master'
-	//custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+	custom_config_version      = 'master'
+	custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
 	config_profile_contact     = null
 	config_profile_url         = null
 
@@ -210,11 +210,11 @@ params {
 includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
-//try {
-//	includeConfig "${params.custom_config_base}/nfcore_custom.config"
-//} catch (Exception e) {
-//	System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-//}
+try {
+	includeConfig "${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")
+}
 
 // Load mskilab-org/nf-jabba custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
@@ -373,7 +373,7 @@ dag {
 
 manifest {
 	name            = 'mskilab-org/nf-jabba'
-	author          = """Tanubrata Dey, Shihab Dider, Joel Rosiene"""
+	author          = """Tanubrata Dey and Shihab Dider"""
 	homePage        = 'https://github.com/mskilab-org/nf-jabba'
 	description     = """Clinical Core Pipeline for MSkiLab"""
 	mainScript      = 'main.nf'