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snystrom / cutNrun-pipeline

Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extensible elsewhere by changing configuration files.
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FragType & NormType aren't correctly detected #11

Open snystrom opened 5 years ago

snystrom commented 5 years ago

sigh power outage right before I hit "submit", so this will be shorter than I'd like.

The issue is basically that at least during the peak calling step (could also be others, need to check) fragtype is detected as '20to120_spikeNor' and normType is detected as 'm'. This results in a the file being correctly named & processed, but this could cause unexpected behavior in the future. The issue appears to be with snakemake autodetecting wildcards.

check: that fragType is entered as '20to120' vs '20to120_' as this type of thing could cause detection issues.

snystrom commented 5 years ago

Set wildcard_contstraints to fix this issue docs here?

snystrom commented 4 years ago

I think I know the cause. 

fragTypes    = ['allFrags', '20to120', '150to700']
normTypeList = ['', '_spikeNorm', '_rpgcNorm']

the '' in normTypeList evaluating to empty string is causing the issue. Best guess. untested.