make.contigs settings

I am trying to run the new MISeq SOP using Illumina data and I am not sure how to include all the fastq files from all my samples within the same command line. For example, if I have 12 fwd and rev fastq files, how do I include all of those files in the make.contigs command? Do I do this on a one by one fashion or do I create a batch command? I assumed I would be able to include all of the files at once, considering the fact that I’m including the .files file with the information for all of the samples.

Have you tried following the MiSeq SOP?