bash bowtie script output with prefix

Question

[Amaranta Remedios]

So I have this bowtie bash script that is working:

#!bin/bash

for a in /Volumes/Norwegian_woods/*.fastq;
do
  Reference=/Volumes/Norwegian_woods/Phaw_5.0;
  bowtie2  -N 1 -p 8 --no-unal -x  ${Reference} -q $a --al ${a%.fastq}_bowtie2.fq -S ${a%.fastq}_bowtie2.sam
done

However, I would like to change the output name and have bowtie2 written as a prefix, looking like this:

bowtie2_${a%.fastq}.fq, bowtie2_${a%.fastq}.sam.

But this is not working. Any suggestion would be appreciated! Thanks

[Asaf]

Nextflow/wdl/snakemake future you will thank you.

[Joe]

Soft quote your variables.

[Amaranta Remedios]

I tried that ('bowtie2_${a%.fastq}.fq') but the outputs now look like this: bowtie2_${a%.fastq}.fq

[Joe]

That's because that's a hard quote, not a soft quote.

I'd advise you to stop here and familiarise yourself with quotes in the shell. It's super important to get this right, especially if this code is going to be run on lots of files by others, or you won't know the input files well. At the moment, any white space in the file names would break this.

http://www.acadix.biz/Unix-guide/HTML/ch02s12.html

Answer 1

[Joe]

Untested, but what you were trying to achieve is:

#!bin/bash

for a in /Volumes/Norwegian_woods/*.fastq;
do
  Reference=/Volumes/Norwegian_woods/Phaw_5.0;
  bowtie2  -N 1 -p 8 --no-unal -x  "${Reference}" -q "$a" --al "${a%.fastq}"_bowtie2.fq -S "${a%.fastq}"_bowtie2.sam
done

Answer 2

[JC]

#!/bin/bash

for a in /Volumes/Norwegian_woods/*.fastq;
do
  Reference=/Volumes/Norwegian_woods/Phaw_5.0
  bowtie2  -N 1 -p 8 --no-unal -x  ${Reference} -q $a --al bowtie2_$(basename $a .fastq).fq -S bowtie2_$(basename $a .fastq).sam
done

Explanation: man basename

Why are you renaming your *fastq to *fq? Sound a bad thing.

[Amaranta Remedios]

Because I will loop again and that makes it easier to recognise just the new files in that folder. Thanks !