I would like to analyze RNAseq with 6 conditions using limma/voom. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates. Ideally, I would like to do a variance estimation using the 6 replicates for the control, and using it compare any two condition C1 vs C2. Does the standard workflow takes care of this?

thanks in advance

Yes, provided you specify the design matrix properly, i.e., in a one-way layout where all replicates for the control condition are in the same group. However, even though limma will handle it, I feel obliged to point out that your set-up is far from ideal; there's no way to spot aberrant behaviour within each of the other conditions if you've only got one replicate for that condition. Thus, you should probably take your DE results with a grain of salt, especially when you're comparing between two conditions.