From e475464f5156b6cce8f1ac8b6a0d459f047ff54c Mon Sep 17 00:00:00 2001 From: Yash Patel Date: Mon, 2 Dec 2024 10:11:55 -0800 Subject: [PATCH] Update configtests --- test/configtest-F16.json | 206 ++++++++++++++++++++------------------- test/configtest-F32.json | 206 ++++++++++++++++++++------------------- 2 files changed, 216 insertions(+), 196 deletions(-) diff --git a/test/configtest-F16.json b/test/configtest-F16.json index e86a9fc..e763202 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -51,6 +51,72 @@ }, "params": { "aligner": "BWA-MEM2-2.2.1", + "base_allocations": { + "deduplicate_records_SAMtools": { + "cpus": "2", + "memory": "27.9 GB" + }, + "extract_GenomeIntervals": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_intermediate_files": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_merged_BAM": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_unmerged_BAMs": { + "cpus": "1", + "memory": "1 GB" + }, + "run_ApplyBQSR_GATK": { + "cpus": "1", + "memory": "2 GB" + }, + "run_BaseRecalibrator_GATK": { + "cpus": "1", + "memory": "27.9 GB" + }, + "run_CalculateContamination_GATK": { + "cpus": "1", + "memory": "14 GB" + }, + "run_DepthOfCoverage_GATK": { + "cpus": "1", + "memory": "14 GB" + }, + "run_GetPileupSummaries_GATK": { + "cpus": "1", + "memory": "14 GB" + }, + "run_IndelRealigner_GATK": { + "cpus": "2", + "memory": "4 GB" + }, + "run_MergeSamFiles_Picard": { + "cpus": "2", + "memory": "27.9 GB" + }, + "run_RealignerTargetCreator_GATK": { + "cpus": "2", + "memory": "4 GB" + }, + "run_SplitIntervals_GATK": { + "cpus": "1", + "memory": "1 GB" + }, + "run_index_SAMtools": { + "cpus": "1", + "memory": "2 GB" + }, + "run_validate_PipeVal": { + "cpus": "1", + "memory": "1 GB" + } + }, "blcds_registered_dataset": false, "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", @@ -89,6 +155,7 @@ "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z", "max_cpus": "16", "max_memory": "31 GB", + "max_time": "24d 20h 31m 24s", "metapipeline_delete_input_bams": false, "metapipeline_states_to_delete": [ "normal", @@ -96,141 +163,78 @@ ], "min_cpus": "1", "min_memory": "1 MB", + "min_time": "1s", "output_dir": "/tmp/outputs", "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1", "parallelize_by_chromosome": true, "patient_id": "TWGSAMIN000001", "picard_version": "2.26.10", "pipeval_version": "4.0.0-rc.2", - "proc_resource_params": { + "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", + "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", + "retry_information": { "deduplicate_records_SAMtools": { - "cpus": "2", - "memory": "27.9 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, - "extract_GenomeIntervals": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_intermediate_files": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_merged_BAM": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_unmerged_BAMs": { - "cpus": "1", - "memory": "1 GB" - }, "run_ApplyBQSR_GATK": { - "cpus": "1", - "memory": "2 GB", - "retry_strategy": { - "memory": { - "operand": "4", - "strategy": "exponential" - } + "memory": { + "operand": "4", + "strategy": "exponential" } }, "run_BaseRecalibrator_GATK": { - "cpus": "1", - "memory": "27.9 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_CalculateContamination_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_DepthOfCoverage_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_GetPileupSummaries_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_IndelRealigner_GATK": { - "cpus": "2", - "memory": "4 GB", - "retry_strategy": { - "memory": { - "operand": "4", - "strategy": "exponential" - } + "memory": { + "operand": "4", + "strategy": "exponential" } }, "run_MergeSamFiles_Picard": { - "cpus": "2", - "memory": "27.9 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_RealignerTargetCreator_GATK": { - "cpus": "2", - "memory": "4 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, - "run_SplitIntervals_GATK": { - "cpus": "1", - "memory": "1 GB" - }, "run_index_SAMtools": { - "cpus": "1", - "memory": "2 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } - }, - "run_validate_PipeVal": { - "cpus": "1", - "memory": "1 GB" } }, - "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", - "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", - "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", "samples_to_process": [ { "id": "4915723", @@ -451,6 +455,12 @@ "enabled": true, "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html" }, + "resource_handler": { + "handle_resources": "closure()", + "set_resource_limit_params": "closure()", + "set_retry": "closure()", + "setup_retry": "closure()" + }, "timeline": { "enabled": true, "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html" diff --git a/test/configtest-F32.json b/test/configtest-F32.json index c25b5da..0ea94bc 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -51,6 +51,72 @@ }, "params": { "aligner": "BWA-MEM2-2.2.1", + "base_allocations": { + "deduplicate_records_SAMtools": { + "cpus": "2", + "memory": "57.6 GB" + }, + "extract_GenomeIntervals": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_intermediate_files": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_merged_BAM": { + "cpus": "1", + "memory": "1 GB" + }, + "remove_unmerged_BAMs": { + "cpus": "1", + "memory": "1 GB" + }, + "run_ApplyBQSR_GATK": { + "cpus": "1", + "memory": "2 GB" + }, + "run_BaseRecalibrator_GATK": { + "cpus": "1", + "memory": "57.6 GB" + }, + "run_CalculateContamination_GATK": { + "cpus": "1", + "memory": "28.8 GB" + }, + "run_DepthOfCoverage_GATK": { + "cpus": "1", + "memory": "28.8 GB" + }, + "run_GetPileupSummaries_GATK": { + "cpus": "1", + "memory": "28.8 GB" + }, + "run_IndelRealigner_GATK": { + "cpus": "4", + "memory": "6 GB" + }, + "run_MergeSamFiles_Picard": { + "cpus": "2", + "memory": "57.6 GB" + }, + "run_RealignerTargetCreator_GATK": { + "cpus": "4", + "memory": "6 GB" + }, + "run_SplitIntervals_GATK": { + "cpus": "1", + "memory": "1 GB" + }, + "run_index_SAMtools": { + "cpus": "1", + "memory": "2 GB" + }, + "run_validate_PipeVal": { + "cpus": "1", + "memory": "1 GB" + } + }, "blcds_registered_dataset": false, "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", @@ -89,6 +155,7 @@ "log_output_dir": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z", "max_cpus": "32", "max_memory": "64 GB", + "max_time": "24d 20h 31m 24s", "metapipeline_delete_input_bams": false, "metapipeline_states_to_delete": [ "normal", @@ -96,141 +163,78 @@ ], "min_cpus": "1", "min_memory": "1 MB", + "min_time": "1s", "output_dir": "/tmp/outputs", "output_dir_base": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/GATK-4.2.4.1", "parallelize_by_chromosome": true, "patient_id": "TWGSAMIN000001", "picard_version": "2.26.10", "pipeval_version": "4.0.0-rc.2", - "proc_resource_params": { + "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", + "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", + "retry_information": { "deduplicate_records_SAMtools": { - "cpus": "2", - "memory": "57.6 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, - "extract_GenomeIntervals": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_intermediate_files": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_merged_BAM": { - "cpus": "1", - "memory": "1 GB" - }, - "remove_unmerged_BAMs": { - "cpus": "1", - "memory": "1 GB" - }, "run_ApplyBQSR_GATK": { - "cpus": "1", - "memory": "2 GB", - "retry_strategy": { - "memory": { - "operand": "4", - "strategy": "exponential" - } + "memory": { + "operand": "4", + "strategy": "exponential" } }, "run_BaseRecalibrator_GATK": { - "cpus": "1", - "memory": "57.6 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_CalculateContamination_GATK": { - "cpus": "1", - "memory": "28.8 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_DepthOfCoverage_GATK": { - "cpus": "1", - "memory": "28.8 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_GetPileupSummaries_GATK": { - "cpus": "1", - "memory": "28.8 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_IndelRealigner_GATK": { - "cpus": "4", - "memory": "6 GB", - "retry_strategy": { - "memory": { - "operand": "4", - "strategy": "exponential" - } + "memory": { + "operand": "4", + "strategy": "exponential" } }, "run_MergeSamFiles_Picard": { - "cpus": "2", - "memory": "57.6 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, "run_RealignerTargetCreator_GATK": { - "cpus": "4", - "memory": "6 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } }, - "run_SplitIntervals_GATK": { - "cpus": "1", - "memory": "1 GB" - }, "run_index_SAMtools": { - "cpus": "1", - "memory": "2 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } + "memory": { + "operand": "2", + "strategy": "exponential" } - }, - "run_validate_PipeVal": { - "cpus": "1", - "memory": "1 GB" } }, - "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", - "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", - "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", "samples_to_process": [ { "id": "4915723", @@ -451,6 +455,12 @@ "enabled": true, "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/report.html" }, + "resource_handler": { + "handle_resources": "closure()", + "set_resource_limit_params": "closure()", + "set_retry": "closure()", + "setup_retry": "closure()" + }, "timeline": { "enabled": true, "file": "/tmp/outputs/recalibrate-BAM-VER.SI.ON/TWGSAMIN000001/log-recalibrate-BAM-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"