When more than two clades are given in the yaml configuration the workflow only uses the last two. I see this behavior in the timeseries workflow but the structure of the 3C workflow looks like it would suffer the same problem. It appears to be a problem with the channel magic, since profiles are generated for all clades but only two are sent to the ProfileMerge process. See timeseries-deconvolute.nf on commit 3780499 to reproduce.
When more than two clades are given in the yaml configuration the workflow only uses the last two. I see this behavior in the timeseries workflow but the structure of the 3C workflow looks like it would suffer the same problem. It appears to be a problem with the channel magic, since profiles are generated for all clades but only two are sent to the ProfileMerge process. See timeseries-deconvolute.nf on commit 3780499 to reproduce.