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Update configtests
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@yashpatel6
yashpatel6 committed Dec 2, 2024
1 parent 19aeeba commit e475464
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Showing 2 changed files with 216 additions and 196 deletions.
206 changes: 108 additions & 98 deletions test/configtest-F16.json
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Original file line number Diff line number Diff line change
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},
"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",
Expand Down Expand Up @@ -89,148 +155,86 @@
"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",
"tumor"
],
"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",
Expand Down Expand Up @@ -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"
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