Usage suggests an option order that generates an error, no outputs, and exit code 0

[hepcat72]

The order of the options in the usage:

Usage: fastq-multx [-g|-l|-B] <barcodes.fil> <read1.fq> -o r1.%.fq [mate.fq -o r2.%.fq] ...

suggests that input files and output file naming templates can be interspersed, such as:

fastq-multx ... read1.fq -o 'r1.%.fq' mate.fq -o 'r2.%.fq'

However, supplying in that order results in the error:

Error: number of input files (1) must match number of output files following '-o'.

and no output files are generated. Whereas this ordering does not generate an error:

fastq-multx ... read1.fq mate.fq -o 'r1.%.fq' -o 'r2.%.fq'

Also, the exit code from a run with the indicated error is 0 (success).

I will likely submit another PR that addresses these and any other issues I encounter in my efforts.

[brwnj]

You've been invited as a collaborator to this repo and may merge pull reqs. Feel free to request a review if you're uncomfortable, but I encourage you to feel free to maintain as you see fit as you're the only one actively updating this.

[hepcat72]

Thanks. I'll be extra careful.