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template.config
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template.config
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// EXECUTION SETTINGS AND GLOBAL DEFAULTS
// External config files import. DO NOT MODIFY THESE LINES!
includeConfig "${projectDir}/config/default.config"
includeConfig "${projectDir}/config/methods.config"
includeConfig "${projectDir}/nextflow.config"
// Inputs/parameters of the pipeline
params {
dataset_id = ''
blcds_registered_dataset = false // if you want the output to be registered
output_dir = '/path/to/output/directory'
// Set to false to disable the publish rule and delete intermediate files as they're no longer needed
// Disable this option for large input BAMs where /scratch space may not be sufficient
save_intermediate_files = false
// Original aligner used to align BAMs
// Provided as <aligner>-<aligner-version>
// Accepted aligners: BWA-MEM2, HISAT2
aligner = 'BWA-MEM2-2.2.1'
// Whether to cache intermediate processes. Set to false by default
// To enable caching, uncomment this option and set to true
// cache_intermediate_pipeline_steps = false
is_emit_original_quals = true // Set to true by default to emit original qualities
is_DOC_run = false // Set to true to run GATK4 DepthOfCoverage, which is very time-consuming for large BAM
// Target intervals to process for DNA panel/targeted sequencing samples
// For WGS, leave this field blank. The intervals will be extracted automatically from the reference dictionary
// For WXS/WES and targeted sequencing samples: provide path to targets in .list, .intervals, BED file, or VCF file format
// Defaults to WGS mode
intervals = ""
// For large samples with disk space issues, uncomment and increase the compression below at the cost of runtime. Range: 0-9
// gatk_ir_compression = 1
// Reference - Used here hg38 decoy version
// GATK requires the reference fasta to be accompanied by a .fai index and .dict dictionary associated with the fasta for fast random access
// These can be found in the same folder as the reference here: /hot/ref/reference/GRCh38-BI-20160721
reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
// Whether to parallelize the pipeline by chromosome or by splitting into equal-sized intervals
// The scatter_count and extra args below only go into effect if parallelize_by_chromosome is disabled
parallelize_by_chromosome = true
scatter_count = 50
split_intervals_extra_args = ''
// GATK bundle - Used here hg38 decoy version
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_known_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz"
bundle_v0_dbsnp138_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz"
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"
// Base resource allocation updater
// See README for adding parameters to update the base resource allocations
}
// Setup the pipeline config. DO NOT REMOVE THIS LINE!
methods.setup()