Rerunning the pipeline after a crash, it crashes on linking fastqs step then reruns the fastqc 

**Describe the bug**
When retuning the pipeline after first crash for any reason, it crashes again wanting to symlink files that are already in the destination. 
I remove the fastq folder then it runs the fastqc again on all samples. 


**Expected behavior**
check if files are in the destination, skip relinking and running fastqc again


