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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?

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According to the information in your question, this should do what you requested:

for i in file1 file2 file3 file4 fileN
do
     function1 "$i"| function2 | function3 > "$i".output
done

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