I am in the process of writing bioinformatics pipelines. These pipelines take in input files and pass them through multiple packages.
Say there is a list of files that goes file1, file2, file3... file n, and for each I want to apply a function that goes function1 -file 1| function 2 | function 3 > file 1.output but want to do it for the whole list of files using a for loop, and allocate file names to the output files accordingly, what commands and syntax should I use?