## template
template_config: ## optional

## input
input_file:
input_file2:
paired_ends: TRUE
quality_encoding: ## will be detected if empty, possible choices: sanger, solexa, illumina1.3, illumina1.5, illumina1.8
subsample_nbreads: ## optional
chunk_size: 1e6
max_nbchunks: ## optional

## output
save_dir:
overwrite_save_dir: never ## possible choices: never, erase, overwrite
prepend_str:
remove_processedfastq: TRUE
remove_chunkdir: TRUE
tmp_dir: ## for temporary chunk_dirs

## system
num_cores: 1
version: ## never set this value manually, will be set for you
chunk_dir: ## never set this value manually, will be set for you

## path
path.genomic_features:
path.gsnap_genomes:

## debug
debug.level: DEBUG ## possible choices: ERROR, WARN, INFO, DEBUG
debug.tracemem: TRUE

## trim reads
trimReads.do: FALSE
trimReads.length:
trimReads.trim5: 0

## filter quality
filterQuality.do: TRUE
filterQuality.minQuality: 23
filterQuality.minFrac: 0.7
filterQuality.minLength:

## detect adapter contamination
detectAdapterContam.do: TRUE
detectAdapterContam.force_paired_end_adapter: FALSE

## detect ribosomal RNA
detectRRNA.do: FALSE
detectRRNA.rrna_genome:

## shortread reports
shortReadReport.do: TRUE
shortReadReport.subsample_nbreads: 20e6 ## optional

## aligner
alignReads.genome:
alignReads.max_mismatches: ## will be determined if empty
alignReads.sam_id:
alignReads.snp_index: ## optional
alignReads.splice_index: ## optional
alignReads.static_parameters: 
alignReads.nbthreads_perchunk: ## optional, if unspecified this value is equal to min(4, num_cores)
alignReads.analyzedBam: uniq ## possible choices: uniq, concordant_uniq
alignReads.use_gmapR_gsnap: TRUE

## mark duplicates
markDuplicates.do: FALSE
path.picard_tools:

## count genomic features
countGenomicFeatures.do: TRUE
countGenomicFeatures.gfeatures:

## coverage
coverage.do: TRUE
coverage.extendReads: FALSE
coverage.fragmentLength:
coverage.maxFragmentLength:

## analyze Variants
analyzeVariants.do: TRUE
analyzeVariants.method: VariantTools ## possible choices: VariantTools, GATK
analyzeVariants.bqual: 23 ## minimum base qual 
analyzeVariants.indels: TRUE
analyzeVariants.rep_mask:    ## path to repeat mask track in bed format
analyzeVariants.dbsnp:    ## path to dbsnp whitelist in vcf format
analyzeVariants.callingFilters: nonRef,nonNRef,readCount,likelihoodRatio ##comma separated list of VT calling Filters
analyzeVariants.postFilters:  ##comma separated list of VT post Filters, for WGS activate avgNborCount
analyzeVariants.positions: ## Path to a GRanges object as RDS used for limiting variant calling on this region
analyzeVariants.genotype: FALSE ## toggles Genotyping via VT
analyzeVariants.vep_options: ## If set toggles vep run

## GATK
path.gatk_genomes:
path.gatk:
gatk.filter_repeats: FALSE ## if TRUE remove vars overlapping with regions in analyzeVariants.rep_mask bed file 
gatk.params:  ## extra gatk params, such as a region filter e.g. -L regions.bed

## realing indels (requires GATK)
realignIndels.do: FALSE
