From de5d3420baf36d27a7737c4befadcda76225c4bf Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 15 Nov 2022 16:11:05 +0100 Subject: [PATCH] increase samtools stats memory --- CHANGELOG.md | 1 + conf/base.config | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c82ecbe95..d0b4236225 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#821](https://github.com/nf-core/sarek/pull/821) - Change `replace` to `putIfAbsent` for automatic search of `input` if none is provided to avoid overwriting values - [#822](https://github.com/nf-core/sarek/pull/822) - Update modules with `nf-core modules update -a`: Update GATK version to 4.3.0 - [#827](https://github.com/nf-core/sarek/pull/827) - Add `--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader` to `GenomicsDB` parameters to speed up the analysis +- [#842](https://github.com/nf-core/sarek/pull/842) - Increase default memory for samtools stats ### Fixed diff --git a/conf/base.config b/conf/base.config index df23e7de7b..bee4acce1a 100644 --- a/conf/base.config +++ b/conf/base.config @@ -54,7 +54,7 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName: 'UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX|SAMTOOLS_STATS' { + withName: 'UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX' { cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } }