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lcdb / lcdb-wf

Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis
https://lcdb.github.io/lcdb-wf
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Note in documentation the need to change 'patterns_targets.py' if not using all three algorithms (macs2, sicer, and spp) in chipseq config #244

Closed hertafeldsr closed 3 years ago

hertafeldsr commented 4 years ago

The file 'patterns_targets.py' expects an entry for each algorithm in the peak_calling section of the config file, as it creates a list ("PEAK_CALLERS = ['macs2', 'spp', 'sicer']") and loops through them to set up the peak calling runs. One solution would be to clarify in the config file the need to edit that list in 'patterns_targets.py' if the user is not using all three algorithms. Another solution would be to edit 'patterns_targets.py' to do some extra parsing of the config file to only loop through algorithms that are listed there.

daler commented 3 years ago

I believe this is fixed in a9afebc0b8909a41d1b1bfeed80c2d80bb33e798