I noticed that the MDS coordinates are not the same across panaroo-qc runs when using the same inputs. A random_state can be specified when calling the sklearn.manifold.MDS method here. I believe that should make the MDS coordinates file deterministic for testing purposes. I suggest giving the user the option to specify an integer for the random_state. The mash_dist.txt report does appear to be deterministic, however.
I noticed that the MDS coordinates are not the same across panaroo-qc runs when using the same inputs. A
random_statecan be specified when calling thesklearn.manifold.MDSmethod here. I believe that should make the MDS coordinates file deterministic for testing purposes. I suggest giving the user the option to specify an integer for therandom_state. Themash_dist.txtreport does appear to be deterministic, however.