diff --git a/CHANGELOG.md b/CHANGELOG.md index fc5927c..3cb7b79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm --- ## [Unreleased] + +--- + +## [9.2.0] - 2022-11-18 +### Added +- `F32.config` for resource allocation ### Changed - Use external resource allocation module - Parameterize Docker registry diff --git a/config/F16.config b/config/F16.config index 30ea84b..442d284 100644 --- a/config/F16.config +++ b/config/F16.config @@ -39,6 +39,10 @@ process { cpus = 2 memory = 4.GB } + withName: deduplicate_records_SAMtools { + cpus = 2 + memory = 4.GB + } withName: run_GetPileupSummaries_GATK { cpus = 1 memory = 5.GB diff --git a/config/F32.config b/config/F32.config new file mode 100644 index 0000000..f795b25 --- /dev/null +++ b/config/F32.config @@ -0,0 +1,94 @@ +process { + withName: run_validate_PipeVal { + cpus = 1 + memory = 1.GB + } + withName: run_HaplotypeCallerVCF_GATK { + cpus = 2 + memory = 4.GB + } + withName: run_HaplotypeCallerGVCF_GATK { + cpus = 2 + memory = 4.GB + } + withName: run_MergeVcfs_Picard { + cpus = 1 + memory = 15.GB + } + withName: run_RealignerTargetCreator_GATK { + cpus = 4 + memory = 6.GB + } + withName: run_IndelRealigner_GATK { + cpus = 4 + memory = 6.GB + } + withName: run_BaseRecalibrator_GATK { + cpus = 1 + memory = 60.GB + } + withName: run_ApplyBQSR_GATK { + cpus = 1 + memory = 1.GB + } + withName: run_index_SAMtools { + cpus = 1 + memory = 1.GB + } + withName: run_MergeSamFiles_Picard { + cpus = 2 + memory = 4.GB + } + withName: deduplicate_records_SAMtools { + cpus = 2 + memory = 4.GB + } + withName: run_GetPileupSummaries_GATK { + cpus = 1 + memory = 5.GB + } + withName: run_CalculateContamination_GATK { + cpus = 1 + memory = 5.GB + } + withName: run_DepthOfCoverage_GATK { + cpus = 1 + memory = 10.GB + } + withName: remove_intermediate_files { + cpus = 1 + memory = 1.GB + } + withName: extract_GenomeIntervals { + cpus = 1 + memory = 1.GB + } + withName: run_SplitIntervals_GATK { + cpus = 1 + memory = 1.GB + } + withName: run_reheader_SAMtools { + cpus = 1 + memory = 1.GB + } + withName: calculate_sha512 { + cpus = 1 + memory = 1.GB + } + withName: run_VariantRecalibratorSNP_GATK { + cpus = 10 + memory = 10.GB + } + withName: run_VariantRecalibratorINDEL_GATK { + cpus = 10 + memory = 10.GB + } + withName: run_ApplyVQSR_GATK { + cpus = 10 + memory = 10.GB + } + withName: filter_gSNP_GATK { + cpus = 10 + memory = 10.GB + } +} diff --git a/nextflow.config b/nextflow.config index 94d67d7..5e26fc3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,5 +5,5 @@ manifest { name = 'call-gSNP' author = ["Yash Patel", "Shu Tao", "Stefan Eng"] description = 'Nextflow pipeline to call germline short variants in single or normal-tumour paired mode' - version = '9.1.0' + version = '9.2.0' }