Merge pull request #37 from nourmahfel/dev

Fix annotsv

Author: nourmahfel

conf/base.config

@@ -8,6 +8,13 @@
 ----------------------------------------------------------------------------------------
 */
 
+
+executor {
+    cpus   = 36       // Total CPUs available on your system
+    memory = '216.GB' // Total memory available on your system
+    queueSize = 10    // Max number of tasks that can be queued/running
+}
+
 process {
 
     // TODO nf-core: Check the defaults for all processes
@@ -19,13 +26,6 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 
-    // Process-specific resource requirements
-    // NOTE - Please try and reuse the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }

conf/modules.config

@@ -666,29 +666,35 @@ process {
     }
 
 
-    withName: 'ANNOTSV_SNIFFLES' {
-        containerOptions = {
-        workflow.containerEngine == 'docker' ? '--user root' : ''
+   withName: 'ANNOTSV_SNIFFLES' {
+   label = 'process_high'
+    containerOptions = {
+            workflow.containerEngine == 'singularity' ?
+            '--writable-tmpfs --bind $PWD --env HOME=$PWD --env TMPDIR=$PWD --env TMP=$PWD' :
+            '--user root'
         }
-        ext.args   = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
-        ext.prefix = { "${meta.id}_annotsv" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/annotsv_sniffles" },
-            mode: 'copy'
-            ]
-            }
+    ext.args   = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
+    ext.prefix = { "${meta.id}_annotsv" }
+    publishDir = [
+        path: { "${params.outdir}/${meta.id}/annotsv_sniffles" },
+        mode: 'copy'
+    ]
+    }
 
-    withName: 'ANNOTSV_SVIM' {
-        containerOptions = {
-        workflow.containerEngine == 'docker' ? '--user root' : ''
+withName: 'ANNOTSV_SVIM' {
+    label = 'process_high'
+    containerOptions = {
+            workflow.containerEngine == 'singularity' ?
+            '--writable-tmpfs --bind $PWD --env HOME=$PWD --env TMPDIR=$PWD --env TMP=$PWD' :
+            '--user root'
         }
-        ext.args   = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
-        ext.prefix = { "${meta.id}_annotsv" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/annotsv_svim" },
-            mode: 'copy'
-            ]
-            }
+    ext.args   = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
+    ext.prefix = { "${meta.id}_annotsv" }
+    publishDir = [
+        path: { "${params.outdir}/${meta.id}/annotsv_svim" },
+        mode: 'copy'
+    ]
+    }
 
     withName: 'UNTAR_ANNOTSV' {
         publishDir = [