Input parameters of script 00 (QC)
Script 00 should take as input parameters the following values:
- single_paired_end = {single; paired}
- library_preparation_kit provided by the backend (please remove any hard-coding of these variables in script 00).
For the adapters: Please download all the adapters from: https://github.com/timflutre/trimmomatic/tree/master/adapters and add the following rules in script 00: If library_preparation_kit contains "Nextera": use NexteraPE-PE.fa for adapters. elseif (library_preparation_kit contains "QIASeq" or "TruSeq") and single_paired_end == "paired": use TruSeq3-PE-2.fa elseif (library_preparation_kit contains "QIASeq" or "TruSeq") and single_paired_end == "single": TruSeq3-SE.fa else return error
Merci beaucoup