Is it possible to pass paired end data on fastqc commandline? 

The 

    ./fastqc --help

 doesn't mention how to do it. It is possible to pass multiple files like

    ./fastq file1 file2 file3

but it doesn't seem to differentiate somehow SE with PE.

On [another post][1] I read that FASTQC is not suited for paired end. However I got confused because inside the  **Configuration/contaminants.txt** file the reads are paired end. 

  [1]: https://www.biostars.org/p/65001/
Normally fastqc will analyse the files for the forward and reverse reads separately.