diff --git a/conf/base.config b/conf/base.config index 1d273c8..f630885 100644 --- 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 index 1fd1408..1cd3c1b 100644 --- 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 "${params.publishdir}", mode: 'copy', pattern: "glimpse_vcf_annotated.vcf.gz.csi" diff --git a/modules/local/split_vcfs/main.nf b/modules/local/split_vcfs/main.nf index fd26dd6..4a6337f 100644 --- a/modules/local/split_vcfs/main.nf +++ b/modules/local/split_vcfs/main.nf @@ -2,6 +2,10 @@ process SPLIT_VCFS { label 'process_medium' + container "${ 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)