Main modules

Version

1.2.4

Date

Dec 17, 2021

There are multiple modules available that perform several steps and generate multiple results.

XICRA modules require several command-line arguments and options to run. There are a number of shared arguments among all modules and some others specific of each module and specified within each one.

• config
• prep
• QC
• trimm
• biotype
• miRNA

Command-line shared arguments

Here we include a brief description of the shared command-line arguments for some of XICRA modules.

Mode:

—project Project mode. Requires as --input a folder containing an initialized BacterialTyper project [Default].

--detached

Isolated mode. --input is a folder containining fastq reads. Provide a unique path o several using --batch option

Input/Output:

—input string Folder containing a project or reads, according to the mode selected. Files could be .fastq/.fq or fastq.gz/.fq.gz. See --help_format for additional details.

--single_end

Single end files [Default OFF]. Default mode is paired-end.

—batch Provide this option if input is a file containing multiple paths instead a path.

--in_sample string

File containing a list of samples to include (one per line) from input folder(s) [Default OFF].

—ex_sample string File containing a list of samples to exclude (one per line) from input folder(s) [Default OFF].

Options:

—threads int Number of CPUs to use [Default: 2]

Additional information:

—debug Show additional message for debugging purposes.

Details of the XICRA project folder

TODO