make.contigs 1 sample sequenced on multiple runs

I have some samples that I need to sequence again to get enough seqs/sample. Can I combine the seqs off the 2 runs through make.contigs

sample1 sample1.run1.f.fastq sample1.run1.r.fastq
sample1 sample1.run2.f.fastq sample1.run2.r.fastq

Will those contigs all be assigned to sample1 or will the second overwrite the first?

They should be pooled into a single sample.

perfect! thanks