diff --git a/workflows/mark04.smk b/workflows/mark04.smk index df8b920d..c69c5a18 100644 --- a/workflows/mark04.smk +++ b/workflows/mark04.smk @@ -11,8 +11,8 @@ from pyggdrasil.tree_inference import CellSimulationId, TreeType, TreeId ################################################################################ # Environment variables -#DATADIR = "/cluster/work/bewi/members/gkoehn/data" -DATADIR = "../data" +DATADIR = "/cluster/work/bewi/members/gkoehn/data" +#DATADIR = "../data" ##################### experiment="mark04" @@ -22,7 +22,7 @@ metrics = ["MP3","AD","DL"] # <-- configure distances here ##################### # Cell Simulation Parameters -num_samples = 30 # <-- configure number of samples here +num_samples = 200 # <-- configure number of samples here # Errors <--- set the error rates here selected_error_cond = ['IDEAL', 'TYPICAL', 'LARGE'] @@ -34,8 +34,8 @@ errors = { name: all_error_cond[name] for name in selected_error_cond } -n_mutations = [30, 5, 10, 50] # <-- configure number of mutations here -n_cells = [200, 1000] #, 5000] # <-- configure number of cells here +n_mutations = [5] #, 10, 30, 50] # <-- configure number of mutations here +n_cells = [200] #, 1000] #, 5000] # <-- configure number of cells here # Homozygous mutations [f: False / t: True] observe_homozygous = "f" # <-- configure whether to observe homozygous mutations here diff --git a/workflows/tree_inference.smk b/workflows/tree_inference.smk index 918ee7f7..e0eaa445 100644 --- a/workflows/tree_inference.smk +++ b/workflows/tree_inference.smk @@ -19,9 +19,9 @@ from pyggdrasil.tree_inference import ( ############################################### ## Relative path from DATADIR to the repo root -#REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil" -REPODIR = ".." -#DATADIR = "/cluster/work/bewi/members/gkoehn/data" +REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil" +#REPODIR = ".." +DATADIR = "/cluster/work/bewi/members/gkoehn/data" ###############################################