From e642e3cd8889f021d68625306fab000ca40a2024 Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Thu, 21 Mar 2024 10:51:25 -0700 Subject: [PATCH 1/5] Revert "Remove failing test" This reverts commit ddfeac0cb61af93b18d88526e939f29fbf5b5f4e. --- test/configtest-new.json | 429 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 429 insertions(+) create mode 100644 test/configtest-new.json diff --git a/test/configtest-new.json b/test/configtest-new.json new file mode 100644 index 00000000..bf18c539 --- /dev/null +++ b/test/configtest-new.json @@ -0,0 +1,429 @@ +{ + "nextflow_version": "23.10.0", + "config": [ + "test/nftest.config" + ], + "params_file": "test/single.yaml", + "cpus": 16, + "memory_gb": 31, + "nf_params": { + "output_dir": "/tmp/outputs" + }, + "envvars": { + "SLURM_JOB_ID": "851543" + }, + "mocks": { + "check_path": "", + "parse_bam_header": { + "read_group": [ + { + "SM": "491572" + } + ] + } + }, + "dated_fields": [ + "params.log_output_dir", + "report.file", + "timeline.file", + "trace.file" + ], + "expected_result": { + "docker": { + "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", + "enabled": true, + "runOptions": "-u $(id -u):$(id -g) $(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", + "uid_and_gid": "-u $(id -u):$(id -g)" + }, + "manifest": { + "author": "Yash Patel, Nicholas Wiltsie", + "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration", + "name": "recalibrate-BAM", + "version": "1.0.0" + }, + "params": { + "aligner": "BWA-MEM2-2.2.1", + "blcds_registered_dataset": false, + "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", + "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", + "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", + "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", + "cache_intermediate_pipeline_steps": false, + "dataset_id": "A-mini", + "docker_container_registry": "ghcr.io/uclahs-cds", + "docker_image_gatk": "broadinstitute/gatk:4.2.4.1", + "docker_image_gatk3": "ghcr.io/uclahs-cds/call-gsnp:GATK-3.7.0", + "docker_image_picard": "ghcr.io/uclahs-cds/picard:2.26.10", + "docker_image_pipeval": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", + "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.17", + "gatk3_version": "GATK-3.7.0", + "gatk_command_mem_diff": "0", + "gatk_ir_compression": "1", + "gatk_version": "4.2.4.1", + "input": { + "BAM": { + "tumor": [ + "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" + ] + }, + "recalibration_table": [ + "/scratch/851543/NO_FILE.grp" + ] + }, + "intervals": "", + "is_DOC_run": false, + "is_emit_original_quals": true, + "is_targeted": false, + "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z", + "max_cpus": "16", + "max_memory": "31 GB", + "metapipeline_delete_input_bams": false, + "metapipeline_states_to_delete": [ + "normal", + "tumor" + ], + "min_cpus": "1", + "min_memory": "1 MB", + "output_dir": "/tmp/outputs", + "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/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": { + "deduplicate_records_SAMtools": { + "cpus": "2", + "memory": "27.9 GB", + "retry_strategy": { + "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" + } + } + }, + "run_BaseRecalibrator_GATK": { + "cpus": "1", + "memory": "27.9 GB", + "retry_strategy": { + "memory": { + "operand": "2", + "strategy": "exponential" + } + } + }, + "run_CalculateContamination_GATK": { + "cpus": "1", + "memory": "14 GB", + "retry_strategy": { + "memory": { + "operand": "2", + "strategy": "exponential" + } + } + }, + "run_DepthOfCoverage_GATK": { + "cpus": "1", + "memory": "14 GB", + "retry_strategy": { + "memory": { + "operand": "2", + "strategy": "exponential" + } + } + }, + "run_GetPileupSummaries_GATK": { + "cpus": "1", + "memory": "14 GB", + "retry_strategy": { + "memory": { + "operand": "2", + "strategy": "exponential" + } + } + }, + "run_IndelRealigner_GATK": { + "cpus": "2", + "memory": "4 GB", + "retry_strategy": { + "memory": { + "operand": "4", + "strategy": "exponential" + } + } + }, + "run_MergeSamFiles_Picard": { + "cpus": "2", + "memory": "27.9 GB", + "retry_strategy": { + "memory": { + "operand": "2", + "strategy": "exponential" + } + } + }, + "run_RealignerTargetCreator_GATK": { + "cpus": "2", + "memory": "4 GB", + "retry_strategy": { + "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" + } + } + }, + "run_validate_PipeVal": { + "cpus": "1", + "memory": "1 GB" + } + }, + "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "samples_to_process": [ + { + "id": "4915723", + "path": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", + "sample_type": "tumor" + } + ], + "samtools_version": "1.17", + "save_intermediate_files": false, + "scatter_count": "50", + "split_intervals_extra_args": "", + "ucla_cds": true, + "use_recal_tables": false, + "work_dir": "/scratch/851543" + }, + "process": { + "cache": false, + "containerOptions": { + "1": "--cpu-shares 1024 --cpus $task.cpus", + "2": "--cpu-shares 1024 --cpus $task.cpus", + "3": "--cpu-shares 1024 --cpus $task.cpus", + "closure": "--cpu-shares 1024 --cpus $task.cpus" + }, + "cpus": { + "1": "1", + "2": "2", + "3": "3", + "closure": "closure()" + }, + "errorStrategy": { + "1": "terminate", + "2": "terminate", + "3": "terminate", + "closure": "terminate" + }, + "executor": "local", + "maxRetries": "1", + "memory": "31 GB", + "withLabel:process_high": { + "cpus": { + "1": "12", + "2": "12", + "3": "12", + "closure": "retry_updater(12, add, 0, $task.attempt, cpus)" + }, + "memory": { + "1": "31 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "retry_updater(84 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withLabel:process_low": { + "cpus": { + "1": "2", + "2": "2", + "3": "2", + "closure": "retry_updater(2, add, 0, $task.attempt, cpus)" + }, + "memory": { + "1": "3 GB", + "2": "6 GB", + "3": "12 GB", + "closure": "retry_updater(3 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withLabel:process_medium": { + "cpus": { + "1": "6", + "2": "6", + "3": "6", + "closure": "retry_updater(6, add, 0, $task.attempt, cpus)" + }, + "memory": { + "1": "31 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "retry_updater(42 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:deduplicate_records_SAMtools": { + "cpus": "2", + "memory": { + "1": "27.9 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "retry_updater(27.9 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:extract_GenomeIntervals": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:remove_intermediate_files": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:remove_merged_BAM": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:remove_unmerged_BAMs": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_ApplyBQSR_GATK": { + "cpus": "1", + "memory": { + "1": "2 GB", + "2": "8 GB", + "3": "31 GB", + "closure": "retry_updater(2 GB, exponential, 4, $task.attempt, memory)" + } + }, + "withName:run_BaseRecalibrator_GATK": { + "cpus": "1", + "memory": { + "1": "27.9 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "retry_updater(27.9 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_CalculateContamination_GATK": { + "cpus": "1", + "memory": { + "1": "14 GB", + "2": "27.9 GB", + "3": "31 GB", + "closure": "retry_updater(14 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_DepthOfCoverage_GATK": { + "cpus": "1", + "memory": { + "1": "14 GB", + "2": "27.9 GB", + "3": "31 GB", + "closure": "retry_updater(14 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_GetPileupSummaries_GATK": { + "cpus": "1", + "memory": { + "1": "14 GB", + "2": "27.9 GB", + "3": "31 GB", + "closure": "retry_updater(14 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_IndelRealigner_GATK": { + "cpus": "2", + "memory": { + "1": "4 GB", + "2": "16 GB", + "3": "31 GB", + "closure": "retry_updater(4 GB, exponential, 4, $task.attempt, memory)" + } + }, + "withName:run_MergeSamFiles_Picard": { + "cpus": "2", + "memory": { + "1": "27.9 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "retry_updater(27.9 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_RealignerTargetCreator_GATK": { + "cpus": "2", + "memory": { + "1": "4 GB", + "2": "8 GB", + "3": "16 GB", + "closure": "retry_updater(4 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_SplitIntervals_GATK": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_index_SAMtools": { + "cpus": "1", + "memory": { + "1": "2 GB", + "2": "4 GB", + "3": "8 GB", + "closure": "retry_updater(2 GB, exponential, 2, $task.attempt, memory)" + } + }, + "withName:run_validate_PipeVal": { + "cpus": "1", + "memory": "1 GB" + } + }, + "report": { + "enabled": true, + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/report.html" + }, + "timeline": { + "enabled": true, + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/timeline.html" + }, + "trace": { + "enabled": true, + "file": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z/nextflow-log/trace.txt" + }, + "workDir": "/scratch/851543" + } +} From e14a75d2098b6423aa380b05be24a1b5fcbf9197 Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Thu, 21 Mar 2024 10:51:33 -0700 Subject: [PATCH 2/5] Revert "Allow workflow to inherit secrets" This reverts commit 35b122f2ea3c5a57d3cada7727970190c9433850. --- .github/workflows/slashcommand.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/slashcommand.yml b/.github/workflows/slashcommand.yml index 9452c6fd..56906bac 100644 --- a/.github/workflows/slashcommand.yml +++ b/.github/workflows/slashcommand.yml @@ -8,4 +8,3 @@ jobs: slashCommandDispatch: if: ${{ github.event.issue.pull_request && startsWith(github.event.comment.body, '/fix-tests') }} uses: uclahs-cds/tool-Nextflow-action/.github/workflows/nextflow-tests.yml@nwiltsie-autofix-tests - secrets: inherit From fb12c1a8d3046cae4f10a72c07cd9fffaa4e6b3c Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Thu, 21 Mar 2024 10:51:42 -0700 Subject: [PATCH 3/5] Revert "Add slash-command workflow" This reverts commit baa967e01a7b613c80d6156fcb2c1e9518171fce. --- .github/workflows/slashcommand.yml | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 .github/workflows/slashcommand.yml diff --git a/.github/workflows/slashcommand.yml b/.github/workflows/slashcommand.yml deleted file mode 100644 index 56906bac..00000000 --- a/.github/workflows/slashcommand.yml +++ /dev/null @@ -1,10 +0,0 @@ -# https://github.com/peter-evans/slash-command-dispatch/blob/a1f5efae7cc1f6c46ef1d02b5ce4710c716907aa/.github/workflows/slash-command-dispatch.yml ---- -name: Slash Command Dispatch -on: - issue_comment: - types: [created] -jobs: - slashCommandDispatch: - if: ${{ github.event.issue.pull_request && startsWith(github.event.comment.body, '/fix-tests') }} - uses: uclahs-cds/tool-Nextflow-action/.github/workflows/nextflow-tests.yml@nwiltsie-autofix-tests From d52cf9b3945e0edec1f2b19812a6d3dfc0b10557 Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Thu, 21 Mar 2024 10:51:43 -0700 Subject: [PATCH 4/5] Revert "Remove CODEOWNERS" This reverts commit 39c5b93c75bda3ef47abb1802ae295c2979f109c. --- .github/CODEOWNERS | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .github/CODEOWNERS diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 00000000..5dd1d560 --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,2 @@ +# Default owner(s) +* @tyamaguchi-ucla @yashpatel6 @Faizal-Eeman From df893a3618ab9fafb0b9ad953d693154dd1c0179 Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Thu, 21 Mar 2024 10:51:51 -0700 Subject: [PATCH 5/5] Revert "Add a failing test directly to main" This reverts commit 028179008e95fde3ac4493ce0e755543fd3cfb9a. --- test/configtest-new.json | 429 --------------------------------------- 1 file changed, 429 deletions(-) delete mode 100644 test/configtest-new.json diff --git a/test/configtest-new.json b/test/configtest-new.json deleted file mode 100644 index bf18c539..00000000 --- a/test/configtest-new.json +++ /dev/null @@ -1,429 +0,0 @@ -{ - "nextflow_version": "23.10.0", - "config": [ - "test/nftest.config" - ], - "params_file": "test/single.yaml", - "cpus": 16, - "memory_gb": 31, - "nf_params": { - "output_dir": "/tmp/outputs" - }, - "envvars": { - "SLURM_JOB_ID": "851543" - }, - "mocks": { - "check_path": "", - "parse_bam_header": { - "read_group": [ - { - "SM": "491572" - } - ] - } - }, - "dated_fields": [ - "params.log_output_dir", - "report.file", - "timeline.file", - "trace.file" - ], - "expected_result": { - "docker": { - "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", - "enabled": true, - "runOptions": "-u $(id -u):$(id -g) $(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", - "uid_and_gid": "-u $(id -u):$(id -g)" - }, - "manifest": { - "author": "Yash Patel, Nicholas Wiltsie", - "description": "Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration", - "name": "recalibrate-BAM", - "version": "1.0.0" - }, - "params": { - "aligner": "BWA-MEM2-2.2.1", - "blcds_registered_dataset": false, - "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", - "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", - "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", - "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", - "cache_intermediate_pipeline_steps": false, - "dataset_id": "A-mini", - "docker_container_registry": "ghcr.io/uclahs-cds", - "docker_image_gatk": "broadinstitute/gatk:4.2.4.1", - "docker_image_gatk3": "ghcr.io/uclahs-cds/call-gsnp:GATK-3.7.0", - "docker_image_picard": "ghcr.io/uclahs-cds/picard:2.26.10", - "docker_image_pipeval": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", - "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.17", - "gatk3_version": "GATK-3.7.0", - "gatk_command_mem_diff": "0", - "gatk_ir_compression": "1", - "gatk_version": "4.2.4.1", - "input": { - "BAM": { - "tumor": [ - "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" - ] - }, - "recalibration_table": [ - "/scratch/851543/NO_FILE.grp" - ] - }, - "intervals": "", - "is_DOC_run": false, - "is_emit_original_quals": true, - "is_targeted": false, - "log_output_dir": "/tmp/outputs/recalibrate-BAM-1.0.0/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-19970704T165655Z", - "max_cpus": "16", - "max_memory": "31 GB", - "metapipeline_delete_input_bams": false, - "metapipeline_states_to_delete": [ - "normal", - "tumor" - ], - "min_cpus": "1", - "min_memory": "1 MB", - "output_dir": "/tmp/outputs", - "output_dir_base": "/tmp/outputs/recalibrate-BAM-1.0.0/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": { - "deduplicate_records_SAMtools": { - "cpus": "2", - "memory": "27.9 GB", - "retry_strategy": { - "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" - } - } - }, - "run_BaseRecalibrator_GATK": { - "cpus": "1", - "memory": "27.9 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } - } - }, - "run_CalculateContamination_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } - } - }, - "run_DepthOfCoverage_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } - } - }, - "run_GetPileupSummaries_GATK": { - "cpus": "1", - "memory": "14 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } - } - }, - "run_IndelRealigner_GATK": { - "cpus": "2", - "memory": "4 GB", - "retry_strategy": { - "memory": { - "operand": "4", - "strategy": "exponential" - } - } - }, - "run_MergeSamFiles_Picard": { - "cpus": "2", - "memory": "27.9 GB", - "retry_strategy": { - "memory": { - "operand": "2", - "strategy": "exponential" - } - } - }, - "run_RealignerTargetCreator_GATK": { - "cpus": "2", - "memory": "4 GB", - "retry_strategy": { - "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" - } - } - }, - "run_validate_PipeVal": { - "cpus": "1", - "memory": "1 GB" - } - }, - "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", - "samples_to_process": [ - { - "id": "4915723", - "path": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", - "sample_type": "tumor" - } - ], - "samtools_version": "1.17", - "save_intermediate_files": false, - "scatter_count": "50", - "split_intervals_extra_args": "", - "ucla_cds": true, - "use_recal_tables": false, - "work_dir": "/scratch/851543" - }, - "process": { - "cache": false, - "containerOptions": { - "1": "--cpu-shares 1024 --cpus $task.cpus", - "2": "--cpu-shares 1024 --cpus $task.cpus", - "3": "--cpu-shares 1024 --cpus $task.cpus", - "closure": "--cpu-shares 1024 --cpus $task.cpus" - }, - "cpus": { - "1": "1", - "2": "2", - "3": "3", - "closure": "closure()" - }, - "errorStrategy": { - "1": "terminate", - "2": "terminate", - "3": "terminate", - "closure": "terminate" - }, - "executor": "local", - "maxRetries": "1", - "memory": "31 GB", - "withLabel:process_high": { - "cpus": { - "1": "12", - "2": "12", - "3": "12", - "closure": "retry_updater(12, add, 0, 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