I am trying to figure out the most efficient method to perform variant analysis on a large dataset. I have 200 samples and forward and reverse reads for a total of 400 fastq files. I was able to load all of these files into Galaxy and create a workflow that looks like this:
fastQ Groomer -> Trim -> BWA-mem -> flagstat -> Generate pileup -> Filter pileup
I have now realized that there is no way to loop through or automate my workflow on my fastq files. Is there a better way to do this other than running this workflow 200 times manually? Can create a script through the command line and use my fastq files as the input? If anyone has any suggestions or is aware of software to handle this type of job I would really appreciate your help.