diff --git a/CHANGELOG.md b/CHANGELOG.md index 04255697..c829ae4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update Nextflow configuration test workflows ### Changed +- Update M64 resource allocations - Update resource allocations ## [8.0.0] - 2024-01-29 diff --git a/config/M64.config b/config/M64.config index 57b902cc..923e4736 100644 --- a/config/M64.config +++ b/config/M64.config @@ -9,87 +9,115 @@ process { if (params.input_type == 'bam') { withName: call_sSNV_SomaticSniper { cpus = 1 - memory = 316.GB + memory = 20.GB + retry_strategy { + memory { + strategy = 'add' + operand = 20.GB + } + } } withName: convert_BAM2Pileup_SAMtools { cpus = 1 - memory = 316.GB + memory = 100.GB + retry_strategy { + memory { + strategy = 'add' + operand = 100.GB + } + } } withName: create_IndelCandidate_SAMtools { cpus = 1 - memory = 316.GB + memory = 10.GB + retry_strategy { + memory { + strategy = 'add' + operand = 10.GB + } + } + } + withName: generate_ReadCount_bam_readcount { + cpus = 1 + memory = 20.GB + retry_strategy { + memory { + strategy = 'add' + operand = 20.GB + } + } } withName: call_sIndel_Manta { - cpus = 36 - memory = 15.GB + cpus = 8 + memory = 10.GB retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 10.GB } } } withName: call_sSNV_Strelka2 { - cpus = 36 - memory = 10.GB + cpus = 28 + memory = 30.GB retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 30.GB } } } withName: call_sSNV_Mutect2 { - cpus = 2 - memory = 5.GB + cpus = 1 + memory = 30.GB retry_strategy { memory { strategy = 'add' - operand = 5.GB + operand = 30.GB } } } withName: run_LearnReadOrientationModel_GATK { - cpus = 4 - memory = 8.GB + cpus = 1 + memory = 30.GB retry_strategy { memory { - strategy = 'exponential' - operand = 2 + strategy = 'add' + operand = 30.GB } } } withName: call_sSNV_MuSE { cpus = 16 - memory = 128.GB + memory = 120.GB retry_strategy { memory { strategy = 'add' - operand = 10.GB + operand = 60.GB } } } withName: run_sump_MuSE { - cpus = 2 - memory = 128.GB + cpus = 6 + memory = 40.GB retry_strategy { memory { strategy = 'add' - operand = 10.GB + operand = 20.GB } } } } withName: plot_VennDiagram_R { - cpus = 1 - memory = 1.GB - retry_strategy { - memory { - strategy = 'add' - operand = 10.GB + cpus = 2 + memory = 5.GB + retry_strategy { + memory { + strategy = 'add' + operand = 10.GB + } } } - } withName: concat_VCFs_BCFtools { cpus = 1 memory = 1.GB diff --git a/config/template.config b/config/template.config index 93cb4d60..cda6978f 100644 --- a/config/template.config +++ b/config/template.config @@ -15,7 +15,6 @@ params { reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' output_dir = '' - work_dir = '' dataset_id = '' // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE