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fixed extension problem and added feature#7
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scottdaniel wants to merge 5 commits intoPennChopMicrobiomeProgram:masterfrom
Open
fixed extension problem and added feature#7scottdaniel wants to merge 5 commits intoPennChopMicrobiomeProgram:masterfrom
scottdaniel wants to merge 5 commits intoPennChopMicrobiomeProgram:masterfrom
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Since we no longer use _R1 as naming convention, updating to use _1
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-Suffixes of .ko files should no longer have _1.fastq
-Added feature where you can put:
organism_filter = [3 or 4 letter code for KEGG genome]
in the json config file, this will filter the m8 files when the ko files are generated
In other words, you will get just the KEGG pathways summaries for that organism
Ex:
I tested with organism_filter = "amu" and got just the annotations for Akkermansia muciniphila
NOTE: the m8 files still shows all the annotations but a simple grep will get you just the one organism