> "scatter_count": "50",

> "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" > }, > "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": "Bool" > }, > "save_interval_list": { > "default": false, > "help": "Whether to save a copy of the interval list generated for picard CollectHsMetrics", > "required": true, > "type": "Bool" > }, > "scatter_count": { > "default": "50", > "help": "How many intervals to divide the genome into for parallelization", > "required": true, > "type": "Integer" > }, > "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": tr

< "workDir": "/scratch/4674821" --- > "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": "Bool" > }, > "save_interval_list": { > "default": false, > "help": "Whether to save a copy of the interval list generated for picard CollectHsMetrics", > "required": true, > "type": "Bool" > }, > "scatter_count": { > "default": "50", > "help": "How many intervals to divide the genome into for parallelization", > "required": true, > "type": "Integer" > }, > "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/targete

Process completed with exit code 82.