Merge pull request #58 from uclahs-cds/kpash-add-plantuml-diagram #15
kiarodAnnotations
10 warnings
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L2
< "nextflow_version": "23.10.0",
< "config": [
< "test/nftest.config"
< ],
< "params_file": "test/single.yaml",
< "cpus": 16,
< "memory_gb": 31,
< "nf_params": {
< "output_dir": "/tmp/nf-config-test-outputs"
---
> "nextflow_version": "23.10.0",
> "config": [
> "test/nftest.config"
> ],
> "params_file": "test/single.yaml",
> "cpus": 16,
> "memory_gb": 31,
> "nf_params": {
> "output_dir": "/tmp/nf-config-test-outputs"
> },
> "envvars": {
> "SLURM_JOB_ID": "4674821"
> },
> "mocks": {
> "check_path": ""
> },
> "dated_fields": [
> "params.log_output_dir",
> "report.file",
> "timeline.file",
> "trace.file",
> "params.date"
> ],
> "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)"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L12
< "envvars": {
< "SLURM_JOB_ID": "4674821"
---
> "manifest": {
> "author": "Nicole Zeltser",
> "description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments",
> "name": "calculate-targeted-coverage",
> "version": "1.0.0-rc.2"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L15
< "mocks": {
< "check_path": ""
---
> "params": {
> "bait_bed": "",
> "bait_interval_list": "",
> "bedr_version": "1.1.0",
> "bedtools_version": "2.29.2",
> "blcds_registered_dataset": false,
> "collect_metrics": true,
> "coverage_cap": "3000",
> "dataset_id": "TWGSAMIN000001-T002-S02-F",
> "dataset_registry_prefix": "/hot/data",
> "date": "19970704T165655Z",
> "dbSNP_slop": "150",
> "docker_container_registry": "ghcr.io/uclahs-cds",
> "docker_image_bedops": "ghcr.io/uclahs-cds/bedr:1.1.0",
> "docker_image_bedtools": "ghcr.io/uclahs-cds/bedtools:2.29.2",
> "docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0",
> "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1",
> "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
> "gatk_command_mem_diff": "2 GB",
> "genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
> "input": {
> "bam": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam"
> },
> "log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z",
> "max_cpus": "16",
> "max_memory": "31 GB",
> "merge_operation": "collapse",
> "min_base_quality": "20",
> "min_cpus": "1",
> "min_mapping_quality": "20",
> "min_memory": "1 MB",
> "min_read_depth": "30",
> "near_distance": "250",
> "off_target_depth": true,
> "off_target_slop": "500",
> "output_dir": "/tmp/nf-config-test-outputs",
> "output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F",
> "output_enriched_target_file": true,
> "patient": "null",
> "picard_CollectHsMetrics_extra_args": "",
> "picard_version": "3.0.0",
> "pipeval_version": "4.0.0-rc.2",
> "reference_dbSNP": "/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz",
> "reference_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
> "sample": "null",
> "sample_id": "TWGSAMIN000001-T002-S02-F",
> "samtools_depth_extra_args": "",
> "samtools_version": "1.16.1",
> "save_all_dbSNP": false,
> "save_intermediate_files": false,
> "save_interval_list": false,
> "save_raw_target_bed": false,
> "target_bed": "/hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/input/GRch38-small.bed",
> "target_depth": true,
> "target_interval_list": "",
> "ucla_cds": true,
> "work_dir": "/scratch/4674821",
> "workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L18
< "dated_fields": [
< "params.log_output_dir",
< "report.file",
< "timeline.file",
< "trace.file",
< "params.date"
< ],
< "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": "Nicole Zeltser",
< "description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments",
< "name": "calculate-targeted-coverage",
< "version": "1.0.0-rc.2"
< },
< "params": {
< "bait_bed": "",
< "bait_interval_list": "",
< "bedr_version": "1.1.0",
< "bedtools_version": "2.29.2",
< "blcds_registered_dataset": false,
< "collect_metrics": true,
< "coverage_cap": "3000",
< "dataset_id": "TWGSAMIN000001-T002-S02-F",
< "dataset_registry_prefix": "/hot/data",
< "date": "19970704T165655Z",
< "dbSNP_slop": "150",
< "docker_container_registry": "ghcr.io/uclahs-cds",
< "docker_image_bedops": "ghcr.io/uclahs-cds/bedr:1.1.0",
< "docker_image_bedtools": "ghcr.io/uclahs-cds/bedtools:2.29.2",
< "docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0",
< "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1",
< "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2",
< "gatk_command_mem_diff": "2 GB",
< "genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
< "input": {
< "bam": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam"
< },
< "log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z",
< "max_cpus": "16",
< "max_memory": "31 GB",
< "merge_operation": "collapse",
< "min_base_quality": "20",
< "min_cpus": "1",
< "min_mapping_quality": "20",
< "min_memory": "1 MB",
< "min_read_depth": "30",
< "near_distance": "250",
< "off_target_depth": true,
< "off_target_slop": "500",
< "output_dir": "/tmp/nf-config-test-outputs",
< "output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F",
< "output_enriched_target_file": true,
< "patient": "null",
< "picard_CollectHsMetrics_extra_args": "",
< "picard_version": "3.0.0",
< "pipeval_version": "4.0.0-rc.2",
< "reference_dbSNP": "/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz",
< "reference_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
< "sample": "null",
< "sample_id": "TWGSAMIN000001-T002-S02-F",
< "samtools_depth_extra_args": "",
< "samtools_version": "1.16.1",
< "save_all_dbSNP": false,
< "save_intermediate_files": false,
< "save_interval_list": false,
< "save_raw_target_bed": false,
< "target_bed": "/hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/input/GRch38-small.bed",
< "target_depth": true,
< "target_interval_list": "",
< "ucla_cds": true,
< "work_dir": "/scratch/4674821",
< "workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
< },
< "params_schema": {
< "bait_bed": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
<
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L205
< "target_depth": {
< "default": false,
< "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
< "required": true,
< "type": "Bool"
---
> "help": "Input samples",
> "required": true,
> "type": "InputNamespace"
> },
> "off_target_depth": {
> "default": true,
> "help": "Whether to calculate depth at off-target dbSNP loci",
> "required": true,
> "type": "Bool"
> },
> "output_dir": {
> "help": "Absolute path to output directory",
> "mode": "w",
> "required": true,
> "type": "Path"
> },
> "output_enriched_target_file": {
> "default": true,
> "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
> "required": true,
> "type": "Bool"
> },
> "picard_CollectHsMetrics_extra_args": {
> "allow_empty": true,
> "help": "Extra arguments for CollectHsMetrics",
> "required": true,
> "type": "String"
> },
> "reference_dbSNP": {
> "help": "Absolute path to thinned dbSNP VCF",
> "mode": "r",
> "required": true,
> "type": "Path"
> },
> "reference_dict": {
> "help": "Absolute path to reference genome dictionary",
> "mode": "r",
> "required": true,
> "type": "Path"
> },
> "sample_id": {
> "help": "Sample ID",
> "required": true,
> "type": "String"
> },
> "samtools_depth_extra_args": {
> "allow_empty": true,
> "help": "Extra arguments for samtools depth",
> "required": true,
> "type": "String"
> },
> "save_intermediate_files": {
> "default": false,
> "help": "Whether to save intermediate files",
> "required": true,
> "type": "Bool"
> },
> "save_interval_list": {
> "default": false,
> "help": "Whether to save a copy of the interval list generated for picard CollectHsMetrics",
> "required": true,
> "type": "Bool"
> },
> "target_bed": {
> "allow_empty": true,
> "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
> "required": true,
> "type": "String"
> },
> "target_depth": {
> "default": false,
> "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
> "required": true,
> "type": "Bool"
> },
> "target_interval_list": {
> "allow_empty": true,
> "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
> "required": true,
> "type": "String"
> }
> },
> "process": {
> "cache": true,
> "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()"
> },
> "echo": true,
> "errorStrategy": {
> "1": "finish",
> "2": "finish",
> "3": "finish",
> "closure": "finish"
> },
> "executor": "local",
> "maxRetries": "1",
> "memory": "31 GB",
> "withLabel:process_high": {
> "cpus": {
> "1": "12",
> "2": "16",
> "3": "16",
> "closure": "closure()"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L211
< "target_interval_list": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
---
> "memory": {
> "1": "31 GB",
> "2": "31 GB",
> "3": "31 GB",
> "closure": "closure()"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L218
< "process": {
< "cache": true,
< "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"
< },
---
> "withLabel:process_low": {
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L227
< "1": "1",
< "2": "2",
< "3": "3",
---
> "1": "2",
> "2": "4",
> "3": "6",
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L232
< "echo": true,
< "errorStrategy": {
< "1": "finish",
< "2": "finish",
< "3": "finish",
< "closure": "finish"
< },
< "executor": "local",
< "maxRetries": "1",
< "memory": "31 GB",
< "withLabel:process_high": {
< "cpus": {
< "1": "12",
< "2": "16",
< "3": "16",
< "closure": "closure()"
< },
< "memory": {
< "1": "31 GB",
< "2": "31 GB",
< "3": "31 GB",
< "closure": "closure()"
< }
< },
< "withLabel:process_low": {
< "cpus": {
< "1": "2",
< "2": "4",
< "3": "6",
< "closure": "closure()"
< },
< "memory": {
< "1": "3 GB",
< "2": "6 GB",
< "3": "9 GB",
< "closure": "closure()"
< }
< },
< "withLabel:process_medium": {
< "cpus": {
< "1": "6",
< "2": "12",
< "3": "16",
< "closure": "closure()"
< },
< "memory": {
< "1": "31 GB",
< "2": "31 GB",
< "3": "31 GB",
< "closure": "closure()"
< }
< },
< "withName:convert_depth_to_bed": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:merge_bedfiles_BEDtools": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:run_BedToIntervalList_picard": {
< "cpus": "1",
< "memory": "3 GB"
< },
< "withName:run_CollectHsMetrics_picard": {
< "cpus": "1",
< "memory": "25 GB"
< },
< "withName:run_depth_SAMtools": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:run_depth_filter": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:run_intersect_BEDtools": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:run_merge_BEDtools": {
< "cpus": "1",
< "memory": "1 GB"
< },
< "withName:run_slop_BEDtools": {
< "cpus": "1",
< "memory": "1 GB"
---
> "memory": {
> "1": "3 GB",
> "2": "6 GB",
> "3": "9 GB",
> "closure": "closure()"
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L321
< "report": {
< "enabled": true,
< "file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/report.html"
< },
< "timeline": {
< "enabled": true,
< "file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/timeline.html"
< },
< "trace": {
< "enabled": true,
< "file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z/nextflow-log/trace.txt"
< },
< "tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]",
< "workDir": "/scratch/4674821",
< "yaml": {
< "bait_bed": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "bait_interval_list": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "collect_metrics": {
< "default": true,
< "help": "Whether to run picard CollectHsMetrics",
< "required": true,
< "type": "Bool"
< },
< "dataset_id": {
< "help": "Dataset ID",
< "required": true,
< "type": "String"
< },
< "genome_sizes": {
< "help": "Absolute path to table of chromosome lengths, can be fasta index",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "input": {
< "elements": {
< "bam": {
< "help": "Input BAM for coverage analysis",
< "mode": "r",
< "required": true,
< "type": "Path"
< }
< },
< "help": "Input samples",
< "required": true,
< "type": "InputNamespace"
< },
< "off_target_depth": {
< "default": true,
< "help": "Whether to calculate depth at off-target dbSNP loci",
< "required": true,
< "type": "Bool"
< },
< "output_dir": {
< "help": "Absolute path to output directory",
< "mode": "w",
< "required": true,
< "type": "Path"
< },
< "output_enriched_target_file": {
< "default": true,
< "help": "Whether or not to output a new target file containing high-coverage off-target dbSNP loci",
< "required": true,
< "type": "Bool"
< },
< "picard_CollectHsMetrics_extra_args": {
< "allow_empty": true,
< "help": "Extra arguments for CollectHsMetrics",
< "required": true,
< "type": "String"
< },
< "reference_dbSNP": {
< "help": "Absolute path to thinned dbSNP VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "reference_dict": {
< "help": "Absolute path to reference genome dictionary",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "sample_id": {
< "help": "Sample ID",
< "required": true,
< "type": "String"
< },
< "samtools_depth_extra_args": {
< "allow_empty": true,
< "help": "Extra arguments for samtools depth",
< "required": true,
< "type": "String"
< },
< "save_intermediate_files": {
< "default": false,
< "help": "Whether to save intermediate files",
< "required": true,
< "type": "B
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Artifacts
Produced during runtime
| Name | Size | |
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test_configtest-F16-out.json
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2.5 KB |
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