update configs

- add container to processes - update error strategy
wtsi-hgi · Sep 17, 2024 · 756159f · 756159f
1 parent 826eba2
commit 756159f
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Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -5,8 +5,8 @@ process {
     memory = { check_max( 2.GB * task.attempt, 'memory' ) }
     time   = { check_max( 1.h  * task.attempt, 'time'   ) }
 
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
-    maxRetries    = 1
+    errorStrategy = { task.attempt <= 3 ? 'retry' : 'finish' }
+    maxRetries    = 3
     maxErrors     = '-1'
 
     // Process-specific resource requirements
@@ -19,7 +19,7 @@ process {
 
     withName: GLIMPSE2_PHASE {
         cpus   = { check_max( 8    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 20.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 20.GB * (task.attempt ** 1.5), 'memory' ) }
         time   = { check_max( 12.h  * task.attempt, 'time'   ) }
     }
 

diff --git a/modules/local/bcftools_impute_info/main.nf b/modules/local/bcftools_impute_info/main.nf
@@ -2,6 +2,10 @@ process BCFTOOLS_IMPUTE_INFO {
 
     label 'process_medium'
 
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
+
     publishDir "${params.publishdir}", mode: 'copy', pattern: "glimpse_vcf_annotated.vcf.gz"
     publishDir "${params.publishdir}", mode: 'copy', pattern: "glimpse_vcf_annotated.vcf.gz.csi"
 

diff --git a/modules/local/split_vcfs/main.nf b/modules/local/split_vcfs/main.nf
@@ -2,6 +2,10 @@ process SPLIT_VCFS {
 
     label 'process_medium'
 
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
+
     input:
     tuple val(meta), path(vcf), path(sample_list)