Configuration Files

Most ProDuSe commands allow arguments to be specified using a configuration INI file. In most cases, this is a much more convenient method of specifying arguments if ProDuSe is to be run multiple times. While you can view more detailed info on config files here, a brief overview will be described here.

Standard Config Files

All config files provided to produse commands (using -c/–config) use the following format:

[Script_Name]
argument=parameter
argument2=parameter2

Where Script_Name is the name of the tool which will use those arguments, with the arguments listed in the section below. Short form argument names are not supported.

Note that config file sections and arguments not relevant to a given tool will safely be ignored, so it is possible to merge config files:

[Trim]
barcode_sequence=NNNWTWYYT
max_mismatch=3

[Pipeline]
reference=genome.fa

A demo sample configuration file can be obtained here.

Note

Argument provided at the command line will override arguments specified in the config file

Sample Configuration Files

When running multiple samples using run_produse, a special sample configuration file is specified instead:

[Sample_Name]
fastqs=/some/path/read.R1.fastq.gz,/some/path/read.R2.fastq.gz

[Sample_Name_2]
fastqs=/some/other/path/read.R1.fastq.gz,/some/other/path/read.R2.fastq.gz

Where Sample_Name is the name used for that sample (this is prepended to all intermediate and output files). Any parameters supported by run_produse can be specified, and will be used for that sample only. For instance:

[Sample_Name_1]
fastqs=/some/path/read.R1.fastq.gz,/some/path/read.R2.fastq.gz
reference=GRCh37.fa

[Sample_Name_2]
fastqs=/some/other/path/read.R1.fastq.gz,/some/other/path/read.R2.fastq.gz
reference=GRCh38.fa

GRCh37 will be used as the reference genome for Sample 1, while GRCh38 will be used for sample 2. Click here to view a demo sample config file

Note

Argument specified in config superseded those specified at either the command line, or by normal config files