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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 {
algorithm = ['stats', 'collectwgsmetrics'] // 'fastqc', 'stats', 'collectwgsmetrics', 'bamqc'
reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
output_dir = '/path/to/output/directory'
blcds_registered_dataset = false // if you want the output to be registered
save_intermediate_files = true
// SAMtools stats options
stats_max_rgs_per_sample = 20
stats_remove_duplicates = false
stats_additional_options = ''
// Picard CollectWgsMetrics options
cwm_coverage_cap = 1000
cwm_minimum_mapping_quality = 20
cwm_minimum_base_quality = 20
cwm_use_fast_algorithm = false
cwm_additional_options = ''
// Qualimap bamqc options
bamqc_output_format = 'pdf' // 'html' or 'pdf'
bamqc_additional_options = ''
// FastQC options
fastqc_level = 'sample' // 'readgroup', 'library' or 'sample'
fastqc_additional_options = ''
// 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()