Allow sample-specific negative control
Opened this issue · 1 comments
snystrom commented
Do something like:
control = lambda wildcards: sampleInfo[sampleInfo.sample == wildcards.sample].control
Maybe (pseudocode):
control_or_default(wildcards, default = CtrlPath):
sampleInfo[sampleInfo.sample == wildcards.sample].control
else CtrlPath
snystrom commented
Consider something like 2 columns:
is_control_id = name or NA (if name, that name = control ID)
control_sample
= name or NA (if name, must be name from is_control_id, that set of samples will be pooled & used as control set)
Then have conditional peak call rules to have discriminative calling step.
Also consider whether peak calls should be made with & without control for additional comparison. Each of these new files gets added to sampleSheet.tsv