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August 3, 2018 13:58
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Arvados WES test submission
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| { | |
| "id": "#main/batch_for_variantcall/analysis", | |
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| { | |
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| "source": "#main/config__algorithm__ensemble" | |
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| { | |
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| "source": "#main/config__algorithm__vcfanno" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/config__algorithm__coverage_interval", | |
| "source": "#main/postprocess_alignment/config__algorithm__coverage_interval" | |
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| { | |
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| "source": "#main/config__algorithm__effects" | |
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| { | |
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| "source": "#main/config__algorithm__min_allele_fraction" | |
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| "source": "#main/config__algorithm__exclude_regions" | |
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| { | |
| "id": "#main/batch_for_variantcall/config__algorithm__variant_regions", | |
| "source": "#main/postprocess_alignment/config__algorithm__variant_regions" | |
| }, | |
| { | |
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| { | |
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| "source": "#main/config__algorithm__validate" | |
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| { | |
| "id": "#main/batch_for_variantcall/config__algorithm__validate_regions", | |
| "source": "#main/config__algorithm__validate_regions" | |
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| { | |
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| "source": "#main/config__algorithm__tools_on" | |
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| { | |
| "id": "#main/batch_for_variantcall/config__algorithm__tools_off", | |
| "source": "#main/config__algorithm__tools_off" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/reference__fasta__base", | |
| "source": "#main/reference__fasta__base" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/reference__twobit", | |
| "source": "#main/reference__twobit" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/reference__rtg", | |
| "source": "#main/reference__rtg" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/reference__genome_context", | |
| "source": "#main/reference__genome_context" | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__cosmic", | |
| "source": "#main/genome_resources__variation__cosmic" | |
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| { | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__clinvar", | |
| "source": "#main/genome_resources__variation__clinvar" | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__lcr", | |
| "source": "#main/genome_resources__variation__lcr" | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__polyx", | |
| "source": "#main/genome_resources__variation__polyx" | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__encode_blacklist", | |
| "source": "#main/genome_resources__variation__encode_blacklist" | |
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| { | |
| "id": "#main/batch_for_variantcall/genome_resources__aliases__ensembl", | |
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| }, | |
| { | |
| "id": "#main/batch_for_variantcall/genome_resources__aliases__human", | |
| "source": "#main/genome_resources__aliases__human" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/genome_resources__aliases__snpeff", | |
| "source": "#main/genome_resources__aliases__snpeff" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/reference__snpeff__hg19", | |
| "source": "#main/reference__snpeff__hg19" | |
| }, | |
| { | |
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| "source": "#main/genome_resources__variation__train_hapmap" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/genome_resources__variation__train_indels", | |
| "source": "#main/genome_resources__variation__train_indels" | |
| }, | |
| { | |
| "id": "#main/batch_for_variantcall/resources", | |
| "source": "#main/resources" | |
| }, | |
| { | |
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| "source": "#main/description" | |
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| { | |
| "id": "#main/batch_for_variantcall/batch_rec" | |
| } | |
| ], | |
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| }, | |
| { | |
| "id": "#main/variantcall", | |
| "in": [ | |
| { | |
| "id": "#main/variantcall/batch_rec", | |
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| ], | |
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| { | |
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| }, | |
| { | |
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| }, | |
| { | |
| "id": "#main/summarize_vc/variants__samples" | |
| }, | |
| { | |
| "id": "#main/summarize_vc/validate__grading_summary" | |
| }, | |
| { | |
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| } | |
| ], | |
| "run": "#summarize_vc.cwl" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec", | |
| "in": [ | |
| { | |
| "id": "#main/qc_to_rec/align_bam", | |
| "source": "#main/postprocess_alignment/align_bam" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/analysis", | |
| "source": "#main/analysis" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/reference__fasta__base", | |
| "source": "#main/reference__fasta__base" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__tools_on", | |
| "source": "#main/config__algorithm__tools_on" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__tools_off", | |
| "source": "#main/config__algorithm__tools_off" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/genome_build", | |
| "source": "#main/genome_build" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__qc", | |
| "source": "#main/config__algorithm__qc" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/metadata__batch", | |
| "source": "#main/metadata__batch" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__coverage_interval", | |
| "source": "#main/postprocess_alignment/config__algorithm__coverage_interval" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__variant_regions__regions", | |
| "source": "#main/postprocess_alignment/depth__variant_regions__regions" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__variant_regions__dist", | |
| "source": "#main/postprocess_alignment/depth__variant_regions__dist" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__samtools__stats", | |
| "source": "#main/postprocess_alignment/depth__samtools__stats" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__samtools__idxstats", | |
| "source": "#main/postprocess_alignment/depth__samtools__idxstats" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__sv_regions__regions", | |
| "source": "#main/postprocess_alignment/depth__sv_regions__regions" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__sv_regions__dist", | |
| "source": "#main/postprocess_alignment/depth__sv_regions__dist" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__coverage__regions", | |
| "source": "#main/postprocess_alignment/depth__coverage__regions" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__coverage__dist", | |
| "source": "#main/postprocess_alignment/depth__coverage__dist" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/depth__coverage__thresholds", | |
| "source": "#main/postprocess_alignment/depth__coverage__thresholds" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__variant_regions", | |
| "source": "#main/postprocess_alignment/config__algorithm__variant_regions" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__variant_regions_merged", | |
| "source": "#main/postprocess_alignment/config__algorithm__variant_regions_merged" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__coverage", | |
| "source": "#main/postprocess_alignment/config__algorithm__coverage" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/config__algorithm__coverage_merged", | |
| "source": "#main/postprocess_alignment/config__algorithm__coverage_merged" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/variants__samples", | |
| "source": "#main/summarize_vc/variants__samples" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/resources", | |
| "source": "#main/resources" | |
| }, | |
| { | |
| "id": "#main/qc_to_rec/description", | |
| "source": "#main/description" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/qc_to_rec/qc_rec" | |
| } | |
| ], | |
| "run": "#qc_to_rec.cwl" | |
| }, | |
| { | |
| "id": "#main/pipeline_summary", | |
| "in": [ | |
| { | |
| "id": "#main/pipeline_summary/qc_rec", | |
| "source": "#main/qc_to_rec/qc_rec" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/pipeline_summary/qcout_rec" | |
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| ], | |
| "run": "#pipeline_summary.cwl", | |
| "scatter": [ | |
| "#main/pipeline_summary/qc_rec" | |
| ], | |
| "scatterMethod": "dotproduct" | |
| }, | |
| { | |
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| "in": [ | |
| { | |
| "id": "#main/multiqc_summary/qcout_rec", | |
| "source": "#main/pipeline_summary/qcout_rec" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#main/multiqc_summary/summary__multiqc" | |
| } | |
| ], | |
| "run": "#multiqc_summary.cwl" | |
| } | |
| ], | |
| "id": "#main" | |
| }, | |
| { | |
| "arguments": [ | |
| { | |
| "position": 0, | |
| "valueFrom": "sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])" | |
| }, | |
| "sentinel_parallel=multi-combined", | |
| "sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;reference__snap__indexes;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample", | |
| "sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__snap__indexes:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__mark_duplicates:var,resources:var,description:var", | |
| "run_number=0" | |
| ], | |
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| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/config__algorithm__exclude_regions", | |
| "type": [ | |
| "null", | |
| "string", | |
| { | |
| "items": [ | |
| "null", | |
| "string" | |
| ], | |
| "type": "array" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/reference__rtg", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/genome_resources__variation__train_indels", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/genome_resources__aliases__snpeff", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/align_bam", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/config__algorithm__variant_regions_merged", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/regions__sample_callable", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec/config__algorithm__callable_regions", | |
| "type": "File" | |
| } | |
| ], | |
| "name": "#wf-variantcall.cwl/batch_rec/batch_rec", | |
| "type": "record" | |
| }, | |
| "type": "array" | |
| } | |
| } | |
| ], | |
| "outputs": [ | |
| { | |
| "id": "#wf-variantcall.cwl/vc_rec", | |
| "outputSource": "#wf-variantcall.cwl/compare_to_rm/vc_rec", | |
| "type": { | |
| "items": { | |
| "fields": [ | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/batch_samples", | |
| "type": [ | |
| "null", | |
| { | |
| "items": "string", | |
| "type": "array" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/validate__summary", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/validate__tp", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/validate__fp", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/validate__fn", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/resources", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/description", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/vrn_file", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/reference__fasta__base", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__vcfanno", | |
| "type": [ | |
| "null", | |
| "string", | |
| { | |
| "items": [ | |
| "null", | |
| "string" | |
| ], | |
| "type": "array" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__variantcaller", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__coverage_interval", | |
| "type": [ | |
| "string", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/metadata__batch", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__min_allele_fraction", | |
| "type": "long" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/reference__genome_context", | |
| "type": { | |
| "items": "File", | |
| "type": "array" | |
| } | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__validate", | |
| "type": [ | |
| "null", | |
| "string", | |
| "File" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/reference__snpeff__hg19", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__validate_regions", | |
| "type": [ | |
| "null", | |
| "string", | |
| "File" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/genome_build", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/metadata__phenotype", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/genome_resources__aliases__human", | |
| "type": [ | |
| "string", | |
| "null", | |
| "boolean" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__tools_off", | |
| "type": { | |
| "items": "string", | |
| "type": "array" | |
| } | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__ensemble", | |
| "type": [ | |
| "null", | |
| "string" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/analysis", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__tools_on", | |
| "type": [ | |
| "null", | |
| "string", | |
| { | |
| "items": [ | |
| "null", | |
| "string" | |
| ], | |
| "type": "array" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__effects", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__variant_regions", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/genome_resources__aliases__ensembl", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__exclude_regions", | |
| "type": [ | |
| "null", | |
| "string", | |
| { | |
| "items": [ | |
| "null", | |
| "string" | |
| ], | |
| "type": "array" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/reference__rtg", | |
| "type": "File" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/genome_resources__aliases__snpeff", | |
| "type": "string" | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__variant_regions_merged", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/regions__sample_callable", | |
| "type": [ | |
| "File", | |
| "null" | |
| ] | |
| }, | |
| { | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec/config__algorithm__callable_regions", | |
| "type": "File" | |
| } | |
| ], | |
| "name": "#wf-variantcall.cwl/vc_rec/vc_rec", | |
| "type": "record" | |
| }, | |
| "type": "array" | |
| } | |
| } | |
| ], | |
| "requirements": [ | |
| { | |
| "class": "EnvVarRequirement", | |
| "envDef": [ | |
| { | |
| "envName": "MPLCONFIGDIR", | |
| "envValue": "." | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "ScatterFeatureRequirement" | |
| }, | |
| { | |
| "class": "SubworkflowFeatureRequirement" | |
| } | |
| ], | |
| "steps": [ | |
| { | |
| "id": "#wf-variantcall.cwl/get_parallel_regions", | |
| "in": [ | |
| { | |
| "id": "#wf-variantcall.cwl/get_parallel_regions/batch_rec", | |
| "source": "#wf-variantcall.cwl/batch_rec" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#wf-variantcall.cwl/get_parallel_regions/region_block" | |
| } | |
| ], | |
| "run": "#get_parallel_regions.cwl" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/variantcall_batch_region", | |
| "in": [ | |
| { | |
| "id": "#wf-variantcall.cwl/variantcall_batch_region/batch_rec", | |
| "source": "#wf-variantcall.cwl/batch_rec" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/variantcall_batch_region/region_block_toolinput", | |
| "source": "#wf-variantcall.cwl/get_parallel_regions/region_block" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#wf-variantcall.cwl/variantcall_batch_region/vrn_file_region" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/variantcall_batch_region/region_block" | |
| } | |
| ], | |
| "run": "#variantcall_batch_region.cwl", | |
| "scatter": [ | |
| "#wf-variantcall.cwl/variantcall_batch_region/region_block_toolinput" | |
| ], | |
| "scatterMethod": "dotproduct" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/concat_batch_variantcalls", | |
| "in": [ | |
| { | |
| "id": "#wf-variantcall.cwl/concat_batch_variantcalls/batch_rec", | |
| "source": "#wf-variantcall.cwl/batch_rec" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/concat_batch_variantcalls/region_block", | |
| "source": "#wf-variantcall.cwl/variantcall_batch_region/region_block" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/concat_batch_variantcalls/vrn_file_region", | |
| "source": "#wf-variantcall.cwl/variantcall_batch_region/vrn_file_region" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#wf-variantcall.cwl/concat_batch_variantcalls/vrn_file" | |
| } | |
| ], | |
| "run": "#concat_batch_variantcalls.cwl" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/postprocess_variants", | |
| "in": [ | |
| { | |
| "id": "#wf-variantcall.cwl/postprocess_variants/batch_rec", | |
| "source": "#wf-variantcall.cwl/batch_rec" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/postprocess_variants/vrn_file_toolinput", | |
| "source": "#wf-variantcall.cwl/concat_batch_variantcalls/vrn_file" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#wf-variantcall.cwl/postprocess_variants/vrn_file" | |
| } | |
| ], | |
| "run": "#postprocess_variants.cwl" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/compare_to_rm", | |
| "in": [ | |
| { | |
| "id": "#wf-variantcall.cwl/compare_to_rm/batch_rec", | |
| "source": "#wf-variantcall.cwl/batch_rec" | |
| }, | |
| { | |
| "id": "#wf-variantcall.cwl/compare_to_rm/vrn_file", | |
| "source": "#wf-variantcall.cwl/postprocess_variants/vrn_file" | |
| } | |
| ], | |
| "out": [ | |
| { | |
| "id": "#wf-variantcall.cwl/compare_to_rm/vc_rec" | |
| } | |
| ], | |
| "run": "#compare_to_rm.cwl" | |
| } | |
| ], | |
| "id": "#wf-variantcall.cwl" | |
| } | |
| ] | |
| } |
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| { | |
| "analysis": [ | |
| "variant2", | |
| "variant2" | |
| ], | |
| "config__algorithm__adapters": [ | |
| [], | |
| [] | |
| ], | |
| "config__algorithm__align_split_size": [ | |
| "null", | |
| "null" | |
| ], | |
| "config__algorithm__aligner": [ | |
| "bwa", | |
| "snap" | |
| ], | |
| "config__algorithm__bam_clean": [ | |
| "False", | |
| "False" | |
| ], | |
| "config__algorithm__coverage_interval": [ | |
| "null", | |
| "null" | |
| ], | |
| "config__algorithm__effects": [ | |
| "snpeff", | |
| "snpeff" | |
| ], | |
| "config__algorithm__ensemble": [ | |
| "null", | |
| "null" | |
| ], | |
| "config__algorithm__exclude_regions": [ | |
| [], | |
| [] | |
| ], | |
| "config__algorithm__mark_duplicates": [ | |
| "True", | |
| "True" | |
| ], | |
| "config__algorithm__min_allele_fraction": [ | |
| 10, | |
| 10 | |
| ], | |
| "config__algorithm__nomap_split_size": [ | |
| 50, | |
| 50 | |
| ], | |
| "config__algorithm__nomap_split_targets": [ | |
| 100, | |
| 100 | |
| ], | |
| "config__algorithm__qc": [ | |
| [ | |
| "fastqc", | |
| "samtools", | |
| "coverage", | |
| "picard", | |
| "qsignature", | |
| "variants", | |
| "contamination", | |
| "peddy" | |
| ], | |
| [ | |
| "fastqc", | |
| "samtools", | |
| "coverage", | |
| "picard", | |
| "qsignature", | |
| "variants", | |
| "contamination", | |
| "peddy", | |
| "viral" | |
| ] | |
| ], | |
| "config__algorithm__recalibrate": [ | |
| "False", | |
| "False" | |
| ], | |
| "config__algorithm__tools_off": [ | |
| [ | |
| "gemini" | |
| ], | |
| [ | |
| "gemini" | |
| ] | |
| ], | |
| "config__algorithm__tools_on": [ | |
| [], | |
| [] | |
| ], | |
| "config__algorithm__trim_reads": [ | |
| "False", | |
| "False" | |
| ], | |
| "config__algorithm__validate": [ | |
| "null", | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/7_100326_FC6107FAAXX-grade.vcf" | |
| } | |
| ], | |
| "config__algorithm__validate_regions": [ | |
| "null", | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/variant_regions-bam.bed" | |
| } | |
| ], | |
| "config__algorithm__variant_regions": [ | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/variant_regions-bam.bed" | |
| }, | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/variant_regions-bam.bed" | |
| } | |
| ], | |
| "config__algorithm__variantcaller": [ | |
| [ | |
| "freebayes", | |
| "vardict" | |
| ], | |
| [ | |
| "freebayes", | |
| "vardict" | |
| ] | |
| ], | |
| "config__algorithm__vcfanno": [ | |
| [], | |
| [] | |
| ], | |
| "description": [ | |
| "Test2", | |
| "Test1" | |
| ], | |
| "files": [ | |
| [ | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/6_100326_FC6107FAAXX.bam", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/6_100326_FC6107FAAXX.bam.bai" | |
| } | |
| ] | |
| } | |
| ], | |
| [ | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/7_100326_FC6107FAAXX.bam", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:a1d976bc7bcba2b523713fa67695d715+464/7_100326_FC6107FAAXX.bam.bai" | |
| } | |
| ] | |
| } | |
| ] | |
| ], | |
| "genome_build": [ | |
| "hg19", | |
| "hg19" | |
| ], | |
| "genome_resources__aliases__ensembl": [ | |
| "homo_sapiens_vep_83_GRCh37", | |
| "homo_sapiens_vep_83_GRCh37" | |
| ], | |
| "genome_resources__aliases__human": [ | |
| "True", | |
| "True" | |
| ], | |
| "genome_resources__aliases__snpeff": [ | |
| "hg19", | |
| "hg19" | |
| ], | |
| "genome_resources__rnaseq__gene_bed": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/rnaseq/ref-transcripts.bed" | |
| }, | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/rnaseq/ref-transcripts.bed" | |
| } | |
| ], | |
| "genome_resources__variation__clinvar": [ | |
| "null", | |
| "null" | |
| ], | |
| "genome_resources__variation__cosmic": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/cosmic-v68-hg19.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/cosmic-v68-hg19.vcf.gz.tbi" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/cosmic-v68-hg19.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/cosmic-v68-hg19.vcf.gz.tbi" | |
| } | |
| ] | |
| } | |
| ], | |
| "genome_resources__variation__dbsnp": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/dbsnp_132.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/dbsnp_132.vcf.gz.tbi" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/dbsnp_132.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/dbsnp_132.vcf.gz.tbi" | |
| } | |
| ] | |
| } | |
| ], | |
| "genome_resources__variation__encode_blacklist": [ | |
| "null", | |
| "null" | |
| ], | |
| "genome_resources__variation__lcr": [ | |
| "null", | |
| "null" | |
| ], | |
| "genome_resources__variation__polyx": [ | |
| "null", | |
| "null" | |
| ], | |
| "genome_resources__variation__train_hapmap": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/hapmap_3.3.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/hapmap_3.3.vcf.gz.tbi" | |
| } | |
| ] | |
| }, | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/hapmap_3.3.vcf.gz", | |
| "secondaryFiles": [ | |
| { | |
| "class": "File", | |
| "path": "keep:9127147c168e27e26738524cbd3a59c6+1633/hg19/variation/hapmap_3.3.vcf.gz.tbi" | |
| } | |
| ] | |
| } | |
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