I want to give two files as input in the following command using loop and generate two respective files as output
File 1: File1_1.fastq.gz
File 2: File1_2.fastq.gz
bbduk.sh -Xmx1g in1= in2= out1= out2= ref=adapters.fa ktrim=r
what did you try ? https://www.google.com/search?q=loop+multiple+variables+bash
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