Bump external/pipeline-Nextflow-config from 1960eaa to f3448ac
#37
dependabot[bot]Annotations
7 errors
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L235
< "params_schema": {
< "aligner": {
< "help": "Aligner used to align input BAMs. Provided as <Aligner>-<Aligner-version>",
< "required": true,
< "type": "AlignerTool"
< },
< "base_resource_update": {
< "elements": {
< "cpus": {
< "help": "List of CPU updates",
< "required": false,
< "type": "ResourceUpdateList"
< },
< "memory": {
< "help": "List of memory updates",
< "required": false,
< "type": "ResourceUpdateList"
< }
< },
< "help": "User-defined modifications for adjusting base resource allocations for processes",
< "required": false,
< "type": "ResourceUpdateNamespace"
< },
< "bundle_contest_hapmap_3p3_vcf_gz": {
< "help": "Absolute path to ConEst HapMap 3p3 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_known_indels_vcf_gz": {
< "help": "Absolute path to known INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": {
< "help": "Absolute path to Mills and 1000g gold standard INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_v0_dbsnp138_vcf_gz": {
< "help": "Absolute path to v0 dbSNP 138 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "dataset_id": {
< "help": "Dataset ID",
< "required": true,
< "type": "String"
< },
< "gatk_ir_compression": {
< "choices": [
< "0",
< "1",
< "2",
< "3",
< "4",
< "5",
< "6",
< "7",
< "8",
< "9"
< ],
< "default": "1",
< "help": "",
< "required": false,
< "type": "Integer"
< },
< "input": {
< "elements": {
< "BAM": {
< "elements": {
< "normal": {
< "help": "Input normal BAMs",
< "required": false,
< "type": "BAMEntryList"
< },
< "tumor": {
< "help": "Input tumor BAMs",
< "required": false,
< "type": "BAMEntryList"
< }
< },
< "help": "Input BAMs for calling",
< "required": true,
< "type": "InputBAMNamespace"
< },
< "recalibration_table": {
< "allow_empty": false,
< "help": "List of any available recalibration tables",
< "required": false,
< "type": "RecalibrationTableList"
< }
< },
< "help": "Input samples",
< "required": true,
< "type": "InputNamespace"
< },
< "intervals": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "is_DOC_run": {
< "default": false,
< "help": "Whether to run the DepthOfCoverage process, which is very time-consuming for large BAMs",
< "required": true,
< "type": "Bool"
< },
< "is_emit_original_quals": {
< "default": true,
< "help": "Whether to emit original quality scores after recalibration",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_delete_input_bams": {
< "default": false,
< "help": "Whether to delete the input BAMs",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_final_output_dir": {
< "help": "Directory containing final outputs to check before input deletion",
< "required": false,
< "type": "String"
< },
< "metapipeline_states_to_delete": {
<
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tests / run (test/configtest-F16.json):
test/configtest-F16.json#L624
< "workDir": "/scratch/851543",
< "yaml": {
< "aligner": {
< "help": "Aligner used to align input BAMs. Provided as <Aligner>-<Aligner-version>",
< "required": true,
< "type": "AlignerTool"
< },
< "base_resource_update": {
< "elements": {
< "cpus": {
< "help": "List of CPU updates",
< "required": false,
< "type": "ResourceUpdateList"
< },
< "memory": {
< "help": "List of memory updates",
< "required": false,
< "type": "ResourceUpdateList"
< }
< },
< "help": "User-defined modifications for adjusting base resource allocations for processes",
< "required": false,
< "type": "ResourceUpdateNamespace"
< },
< "bundle_contest_hapmap_3p3_vcf_gz": {
< "help": "Absolute path to ConEst HapMap 3p3 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_known_indels_vcf_gz": {
< "help": "Absolute path to known INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": {
< "help": "Absolute path to Mills and 1000g gold standard INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_v0_dbsnp138_vcf_gz": {
< "help": "Absolute path to v0 dbSNP 138 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "dataset_id": {
< "help": "Dataset ID",
< "required": true,
< "type": "String"
< },
< "gatk_ir_compression": {
< "choices": [
< "0",
< "1",
< "2",
< "3",
< "4",
< "5",
< "6",
< "7",
< "8",
< "9"
< ],
< "default": "1",
< "help": "",
< "required": false,
< "type": "Integer"
< },
< "input": {
< "elements": {
< "BAM": {
< "elements": {
< "normal": {
< "help": "Input normal BAMs",
< "required": false,
< "type": "BAMEntryList"
< },
< "tumor": {
< "help": "Input tumor BAMs",
< "required": false,
< "type": "BAMEntryList"
< }
< },
< "help": "Input BAMs for calling",
< "required": true,
< "type": "InputBAMNamespace"
< },
< "recalibration_table": {
< "allow_empty": false,
< "help": "List of any available recalibration tables",
< "required": false,
< "type": "RecalibrationTableList"
< }
< },
< "help": "Input samples",
< "required": true,
< "type": "InputNamespace"
< },
< "intervals": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "is_DOC_run": {
< "default": false,
< "help": "Whether to run the DepthOfCoverage process, which is very time-consuming for large BAMs",
< "required": true,
< "type": "Bool"
< },
< "is_emit_original_quals": {
< "default": true,
< "help": "Whether to emit original quality scores after recalibration",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_delete_input_bams": {
< "default": false,
< "help": "Whether to delete the input BAMs",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_final_output_dir": {
< "help": "Directory containing final outputs to check before input deletion",
< "required": false,
< "type": "String"
< },
< "metapipeline_
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tests / run (test/configtest-F16.json)
Process completed with exit code 82.
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tests / run (test/configtest-F32.json):
test/configtest-F32.json#L235
< "params_schema": {
< "aligner": {
< "help": "Aligner used to align input BAMs. Provided as <Aligner>-<Aligner-version>",
< "required": true,
< "type": "AlignerTool"
< },
< "base_resource_update": {
< "elements": {
< "cpus": {
< "help": "List of CPU updates",
< "required": false,
< "type": "ResourceUpdateList"
< },
< "memory": {
< "help": "List of memory updates",
< "required": false,
< "type": "ResourceUpdateList"
< }
< },
< "help": "User-defined modifications for adjusting base resource allocations for processes",
< "required": false,
< "type": "ResourceUpdateNamespace"
< },
< "bundle_contest_hapmap_3p3_vcf_gz": {
< "help": "Absolute path to ConEst HapMap 3p3 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_known_indels_vcf_gz": {
< "help": "Absolute path to known INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": {
< "help": "Absolute path to Mills and 1000g gold standard INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_v0_dbsnp138_vcf_gz": {
< "help": "Absolute path to v0 dbSNP 138 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "dataset_id": {
< "help": "Dataset ID",
< "required": true,
< "type": "String"
< },
< "gatk_ir_compression": {
< "choices": [
< "0",
< "1",
< "2",
< "3",
< "4",
< "5",
< "6",
< "7",
< "8",
< "9"
< ],
< "default": "1",
< "help": "",
< "required": false,
< "type": "Integer"
< },
< "input": {
< "elements": {
< "BAM": {
< "elements": {
< "normal": {
< "help": "Input normal BAMs",
< "required": false,
< "type": "BAMEntryList"
< },
< "tumor": {
< "help": "Input tumor BAMs",
< "required": false,
< "type": "BAMEntryList"
< }
< },
< "help": "Input BAMs for calling",
< "required": true,
< "type": "InputBAMNamespace"
< },
< "recalibration_table": {
< "allow_empty": false,
< "help": "List of any available recalibration tables",
< "required": false,
< "type": "RecalibrationTableList"
< }
< },
< "help": "Input samples",
< "required": true,
< "type": "InputNamespace"
< },
< "intervals": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "is_DOC_run": {
< "default": false,
< "help": "Whether to run the DepthOfCoverage process, which is very time-consuming for large BAMs",
< "required": true,
< "type": "Bool"
< },
< "is_emit_original_quals": {
< "default": true,
< "help": "Whether to emit original quality scores after recalibration",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_delete_input_bams": {
< "default": false,
< "help": "Whether to delete the input BAMs",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_final_output_dir": {
< "help": "Directory containing final outputs to check before input deletion",
< "required": false,
< "type": "String"
< },
< "metapipeline_states_to_delete": {
<
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tests / run (test/configtest-F32.json):
test/configtest-F32.json#L624
< "workDir": "/scratch/851543",
< "yaml": {
< "aligner": {
< "help": "Aligner used to align input BAMs. Provided as <Aligner>-<Aligner-version>",
< "required": true,
< "type": "AlignerTool"
< },
< "base_resource_update": {
< "elements": {
< "cpus": {
< "help": "List of CPU updates",
< "required": false,
< "type": "ResourceUpdateList"
< },
< "memory": {
< "help": "List of memory updates",
< "required": false,
< "type": "ResourceUpdateList"
< }
< },
< "help": "User-defined modifications for adjusting base resource allocations for processes",
< "required": false,
< "type": "ResourceUpdateNamespace"
< },
< "bundle_contest_hapmap_3p3_vcf_gz": {
< "help": "Absolute path to ConEst HapMap 3p3 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_known_indels_vcf_gz": {
< "help": "Absolute path to known INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": {
< "help": "Absolute path to Mills and 1000g gold standard INDELs VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "bundle_v0_dbsnp138_vcf_gz": {
< "help": "Absolute path to v0 dbSNP 138 VCF",
< "mode": "r",
< "required": true,
< "type": "Path"
< },
< "dataset_id": {
< "help": "Dataset ID",
< "required": true,
< "type": "String"
< },
< "gatk_ir_compression": {
< "choices": [
< "0",
< "1",
< "2",
< "3",
< "4",
< "5",
< "6",
< "7",
< "8",
< "9"
< ],
< "default": "1",
< "help": "",
< "required": false,
< "type": "Integer"
< },
< "input": {
< "elements": {
< "BAM": {
< "elements": {
< "normal": {
< "help": "Input normal BAMs",
< "required": false,
< "type": "BAMEntryList"
< },
< "tumor": {
< "help": "Input tumor BAMs",
< "required": false,
< "type": "BAMEntryList"
< }
< },
< "help": "Input BAMs for calling",
< "required": true,
< "type": "InputBAMNamespace"
< },
< "recalibration_table": {
< "allow_empty": false,
< "help": "List of any available recalibration tables",
< "required": false,
< "type": "RecalibrationTableList"
< }
< },
< "help": "Input samples",
< "required": true,
< "type": "InputNamespace"
< },
< "intervals": {
< "allow_empty": true,
< "help": "Target intervals to process for DNA panel/targeted sequencing samples; leave empty for WGS",
< "required": true,
< "type": "String"
< },
< "is_DOC_run": {
< "default": false,
< "help": "Whether to run the DepthOfCoverage process, which is very time-consuming for large BAMs",
< "required": true,
< "type": "Bool"
< },
< "is_emit_original_quals": {
< "default": true,
< "help": "Whether to emit original quality scores after recalibration",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_delete_input_bams": {
< "default": false,
< "help": "Whether to delete the input BAMs",
< "required": true,
< "type": "Bool"
< },
< "metapipeline_final_output_dir": {
< "help": "Directory containing final outputs to check before input deletion",
< "required": false,
< "type": "String"
< },
< "metapipeline_
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tests / run (test/configtest-F32.json)
Process completed with exit code 82.
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tests / summary
Tests failed!
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
|
test_configtest-F16-out.json
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2.45 KB |
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test_configtest-F32-out.json
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2.46 KB |
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