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edmundmilleredmundmiller
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test: Add a test for benchmarking failed_tasks
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‎modules/local/benchmark_report/tests/main.nf.test‎

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nextflow_process {
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name "Test Process BENCHMARK_REPORT"
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script "../main.nf"
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process "BENCHMARK_REPORT"
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// TODO: Should run without AWS cost report
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test("Should run with removing failed tasks") {
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when {
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process {
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"""
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input[0] = [file("modules/local/benchmark_report/tests/runs_dump/4Bi5xBK6E2Nbhj")]
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input[1] = ["group1"]
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input[2] = []
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input[3] = true
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"""
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}
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}
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then {
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assert process.success
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assert snapshot(process.out).match()
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assert path(process.out.benchmark_html.get(0)).exists()
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assert path(process.out.versions.get(0)).exists()
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}
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}
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// TODO: Should run with multiple runs
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// TODO: Should run with AWS cost report
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// TODO: Should run with remove failed tasks
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}

‎modules/local/benchmark_report/tests/runs_dump/4Bi5xBK6E2Nbhj/service-info.json‎

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{
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"version" : "24.3.0-cycle3",
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"apiVersion" : "1.25.0",
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"commitId" : "58b72a7",
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"authTypes" : [ "auth0", "email" ],
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"loginPath" : "/login",
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"navbar" : {
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"menus" : [ {
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"label" : "Docs",
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"url" : "https://docs.seqera.io"
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}, {
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"label" : "Community",
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"url" : "https://community.seqera.io/"
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}, {
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"label" : "Feedback",
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"url" : "https://feedback.seqera.io/"
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} ]
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},
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"heartbeatInterval" : 3960,
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"userWorkspaceEnabled" : true,
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"allowInstanceCredentials" : false,
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"landingUrl" : "https://seqera.io",
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"termsOfUseUrl" : "https://seqera.io/legal/terms-of-use",
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"contentUrl" : "https://user-data.cloud.seqera.io",
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"analytics" : { },
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"allowLocalRepos" : true,
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"contentMaxFileSize" : 26214400,
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"waveEnabled" : true,
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"groundswellEnabled" : true,
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"forgePrefix" : "TowerForge",
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"seqeraCloud" : true,
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"evalWorkspaceIds" : [ 40230138858677 ]
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}

‎modules/local/benchmark_report/tests/runs_dump/4Bi5xBK6E2Nbhj/workflow-launch.json‎

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{
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"id" : "60fj4f5UEugLFrdDHOjYGJ",
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"computeEnv" : {
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"id" : "4gVZCvyQkFBGLAq8Vh1q2E",
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"name" : "deleted-6691228547460385",
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"platform" : "aws-batch",
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"config" : {
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"region" : "eu-west-1",
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"computeQueue" : "TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-work",
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"executionRole" : "arn:aws:iam::893329243595:role/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-ExecutionRole",
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"headQueue" : "TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-head",
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"headJobRole" : "arn:aws:iam::893329243595:role/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-FargateRole",
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"volumes" : [ ],
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"workDir" : "s3://nf-tower-bucket",
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"waveEnabled" : true,
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"fusion2Enabled" : true,
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"nvnmeStorageEnabled" : true,
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"forge" : {
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"type" : "SPOT",
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"minCpus" : 0,
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"maxCpus" : 500,
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"gpuEnabled" : false,
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"instanceTypes" : [ "c6id", "m6id", "r6id" ],
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"subnets" : [ ],
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"securityGroups" : [ ],
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"disposeOnDeletion" : true,
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"allowBuckets" : [ ],
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"efsCreate" : false,
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"fargateHeadEnabled" : true,
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"arm64Enabled" : false
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},
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"forgedResources" : [ {
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"IamRole" : "arn:aws:iam::893329243595:role/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-ServiceRole"
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}, {
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"IamRole" : "arn:aws:iam::893329243595:role/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-ExecutionRole"
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}, {
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"IamInstanceProfile" : "arn:aws:iam::893329243595:instance-profile/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-InstanceRole"
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}, {
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"IamRole" : "arn:aws:iam::893329243595:role/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-FargateRole"
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}, {
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"BatchEnv" : "arn:aws:batch:eu-west-1:893329243595:compute-environment/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-head"
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}, {
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"BatchQueue" : "arn:aws:batch:eu-west-1:893329243595:job-queue/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-head"
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}, {
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"Ec2LaunchTemplate" : "TowerForge-4gVZCvyQkFBGLAq8Vh1q2E"
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}, {
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"BatchEnv" : "arn:aws:batch:eu-west-1:893329243595:compute-environment/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-work"
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}, {
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"BatchQueue" : "arn:aws:batch:eu-west-1:893329243595:job-queue/TowerForge-4gVZCvyQkFBGLAq8Vh1q2E-work"
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} ],
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"discriminator" : "aws-batch"
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},
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"dateCreated" : "2023-08-03T08:49:11Z",
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"lastUpdated" : "2024-09-24T08:52:40Z",
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"lastUsed" : "2024-09-24T02:31:15Z",
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"deleted" : true,
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"status" : "INVALID",
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"message" : "Compute environment has been deleted",
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"credentialsId" : "5R5EMRNv0M8DXAiJ4WkMH9",
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"orgId" : 187965850823746,
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"workspaceId" : 40230138858677
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},
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"pipeline" : "https://github.com/nf-core/rnaseq",
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"workDir" : "s3://nf-tower-bucket",
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"revision" : "3.12.0",
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"configText" : "",
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"towerConfig" : "",
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"paramsText" : "{\"input\":\"https://api.tower.nf/workspaces/40230138858677/datasets/66XmaViCT87OV8aGYS2Pk1/v/1/n/samplesheet_test.csv\",\"outdir\":\"s3://nf-tower-bucket/rnaseq/crazy_wiles/results\",\"save_merged_fastq\":false,\"with_umi\":false,\"umitools_extract_method\":\"string\",\"skip_umi_extract\":false,\"umitools_bc_pattern\":\"NNNN\",\"umitools_grouping_method\":\"directional\",\"umitools_dedup_stats\":false,\"save_umi_intermeds\":false,\"bbsplit_fasta_list\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt\",\"save_bbsplit_reads\":false,\"skip_bbsplit\":false,\"remove_ribo_rna\":false,\"ribo_database_manifest\":\"${projectDir}/assets/rrna-db-defaults.txt\",\"save_non_ribo_reads\":false,\"fasta\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta\",\"gtf\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz\",\"gff\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz\",\"transcript_fasta\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta\",\"additional_fasta\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz\",\"hisat2_index\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz\",\"rsem_index\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz\",\"salmon_index\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz\",\"hisat2_build_memory\":\"200.GB\",\"gencode\":false,\"gtf_extra_attributes\":\"gene_name\",\"gtf_group_features\":\"gene_id\",\"featurecounts_group_type\":\"gene_biotype\",\"featurecounts_feature_type\":\"exon\",\"save_reference\":false,\"igenomes_base\":\"s3://ngi-igenomes/igenomes\",\"igenomes_ignore\":false,\"trimmer\":\"trimgalore\",\"min_trimmed_reads\":10000,\"skip_trimming\":false,\"save_trimmed\":false,\"aligner\":\"star_salmon\",\"pseudo_aligner\":\"salmon\",\"bam_csi_index\":false,\"star_ignore_sjdbgtf\":false,\"min_mapped_reads\":5,\"stringtie_ignore_gtf\":false,\"save_unaligned\":false,\"save_align_intermeds\":false,\"skip_markduplicates\":false,\"skip_alignment\":false,\"skip_pseudo_alignment\":false,\"rseqc_modules\":\"bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication\",\"deseq2_vst\":true,\"skip_bigwig\":false,\"skip_stringtie\":false,\"skip_fastqc\":false,\"skip_preseq\":true,\"skip_dupradar\":false,\"skip_qualimap\":false,\"skip_rseqc\":false,\"skip_biotype_qc\":false,\"skip_deseq2_qc\":false,\"skip_multiqc\":false,\"skip_qc\":false,\"custom_config_version\":\"master\",\"custom_config_base\":\"https://raw.githubusercontent.com/nf-core/configs/master\",\"config_profile_name\":\"Test profile\",\"config_profile_description\":\"Minimal test dataset to check pipeline function\",\"test_data_base\":\"https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3\",\"max_cpus\":2,\"max_memory\":\"6.GB\",\"max_time\":\"6.h\",\"help\":false,\"version\":false,\"publish_dir_mode\":\"copy\",\"plaintext_email\":false,\"max_multiqc_email_size\":\"25.MB\",\"monochrome_logs\":false,\"validate_params\":true,\"show_hidden_params\":false}",
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"preRunScript" : "export CAPSULE_LOG=none\nexport NXF_VER=23.08.0-edge\nexport NXF_FILE_ROOT=s3://nf-tower-bucket/scratch/$TOWER_WORKFLOW_ID",
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"resume" : false,
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"pullLatest" : false,
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"stubRun" : false,
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"runName" : "crazy_wiles",
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"configProfiles" : [ "test" ],
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"dateCreated" : "2023-05-19T09:26:56Z",
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"lastUpdated" : "2023-10-24T04:36:41Z"
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}

‎modules/local/benchmark_report/tests/runs_dump/4Bi5xBK6E2Nbhj/workflow-load.json‎

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{
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"pending" : 0,
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"submitted" : 0,
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"running" : 0,
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"succeeded" : 192,
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"failed" : 0,
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"cached" : 0,
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"memoryEfficiency" : 2.8175535,
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"cpuEfficiency" : 62.696598,
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"cpus" : 325,
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"cpuTime" : 2296938,
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"cpuLoad" : 1440102,
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"memoryRss" : 34851745792,
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"memoryReq" : 1236950581248,
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"readBytes" : 5459289730,
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"writeBytes" : 1022126896,
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"volCtxSwitch" : 36821,
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"invCtxSwitch" : 44046,
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"cost" : 0.0202211975,
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"loadTasks" : 0,
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"loadCpus" : 0,
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"loadMemory" : 0,
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"peakCpus" : 18,
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"peakTasks" : 9,
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"peakMemory" : 57982058496,
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"executors" : [ "awsbatch" ],
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"dateCreated" : "2023-10-24T04:39:27Z",
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"lastUpdated" : "2023-10-24T04:39:27Z"
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}

‎modules/local/benchmark_report/tests/runs_dump/4Bi5xBK6E2Nbhj/workflow-metadata.json‎

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{
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"pipelineId" : 189046775836482,
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"workspaceId" : 40230138858677,
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"workspaceName" : "showcase",
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"userId" : 10003,
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"runUrl" : "https://tower.nf/orgs/community/workspaces/showcase/watch/4Bi5xBK6E2Nbhj"
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}

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