Bash: replace part of filename

Question

I have a command I want to run on all of the files of a folder, and the command\'s syntax looks like this:

tophat -o  
         


        

Answer 1

Not an answer but a suggestion: as a bioinformatician, you shoud use GNU make and its option -j (number of parallel jobs). The Makefile would be:

.PHONY:all
FASTQS=$(shell ls *.fastq)

%.bam: %.fastq
    tophat -o $@ $<

all:  $(FASTQS:.bam=.fastq)