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MARK01 Rerun with new Error Rates #167

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Sep 4, 2023
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MARK01 Rerun with new Error Rates #167

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12 changes: 6 additions & 6 deletions workflows/mark01.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -11,18 +11,18 @@ 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="mark01"

# Metrics: Distances / Similarity Measure to use
metrics = ["MP3","AD","DL"] # <-- configure distances here
metrics = ["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']
Expand All @@ -34,7 +34,7 @@ errors = {
name: all_error_cond[name]
for name in selected_error_cond
}
n_mutations = [30] #5, 10, 50] # <-- configure number of mutations 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]
Expand All @@ -46,7 +46,7 @@ cell_attachment_strategy = "UXR" # <-- configure cell attachment strategy here
#####################
# True Tree Parameters
tree_types = ["r"]#, "s"] # <-- configure tree type here ["r","s","d"]
tree_seeds = [42,]# 34] # <-- configure tree seed here
tree_seeds = [42, 34] # <-- configure tree seed here

#####################
# Auxiliary variables
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