prep

This module prepares fastq files for later usage.

It initially checks the length of the name and advises the user to rename samples if exceeded a length (10 characters). Along XICRA there are a few string length limitations by different software that need to be sort out from the beginning of the process.

See additional details of this name format limitations under user-guide section: format fastq files

Once sample names are checked this module allows the user to copy files into the project folder initiate or only link them using a symbolic link to avoid duplicated raw data.

If using the the --project option, this module would create a single folder for each sample and a folder named as raw including the linked or copied fastq files. See additional details of project folder organization here.