Merge pull request #1 from wtsi-hgi/jo_edits

Update configs
wtsi-hgi · Sep 17, 2024 · 1581ad6 · 1581ad6
2 parents bca7ea8 + 756159f
commit 1581ad6
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diff --git a/conf/base.config b/conf/base.config
@@ -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)