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simonrharris / SKA

Split Kmer Analysis
MIT License
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Is there a looping command to perform all SKA task #25

Closed foamy1881 closed 4 years ago

foamy1881 commented 4 years ago

Anyone have any looping command i.e. like python script to perform the task from raw fastq folder? I have like hundreds of isolates..

tseemann commented 4 years ago

I find GNU parallel is good for that, even if you do one at a time.

parallel "ska something -out {}.output {}/R1.fq.gz {}/R2.fq.gz" < file_of_Ids.txt