Parameters

This page describes all command-line arguments and parameters available in ViralFlow.

Parameter File

ViralFlow requires a parameter file that contains all configuration options. Example parameter files can be found in the test_files directory.

Parameter Reference

Argument	Default Value	Description
virus	sars-cov2	Analysis type (sars-cov2 or custom)
primersBED	null	Absolute path to bed file with primers information used in genomic amplification (optional)
outDir	launchDir/output/	Absolute path to the directory where the results will be stored
inDir	launchDir/input/	Absolute path to the directory with the input data (directory with the FASTQ files)
runSnpEff	true	Needed to run the snpEff tool (true or false)
writeMappedReads	true	Needed to generate the FASTQ files containing the sequencing reads that mapped to the reference genome
minLen	75	Minimum size the reads must have. Reads below this threshold will be eliminated by FastP
depth	5	Minimum coverage depth to call consensus bases. Positions with lower coverage depth will not be called and a “-” will be added to the respective consensus genomic position
mapping_quality	30	Mapping quality threshold used to variant calling
base_quality	30	Base quality threshold used to variant calling
minDpIntrahost	100	Minimum coverage depth per genomic site to be considered in the intrahost analysis
trimLen	0	Number of bases that should be trimmed at both ends of the reads
refGenomeCode	null	Code of the genome to be used in the custom analysis
referenceGFF	null	GFF genome file to be used in custom analysis
referenceGenome	null	Fasta genome file to be used in custom analysis
nextflowSimCalls	null	Number of simultaneous calls that nextflow can perform
fastp_threads	1	Number of threads to be used in the fastp read filtering step
bwa_threads	1	Number of threads to be used in the bwa mapping step
mafft_threads	1	Number of threads to be used in the mafft alignment step
dedup	false	This argument enable dedup mode of fastp. To activate it change value to true on params test file
ndedup	3	When dedup mode is active you can use accuracy levels (1 - 6). You can change this value, but we recommend the standard. How much higher, more RAM and time are consumed. To activate it change value from 1 to 6 on params test file