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error: Found argument 'file.fastq' which wasn't expected, or isn't valid in this context #10

@dgslos

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@dgslos

Wanted behavior: Run chopper directly on input files


I noticed that I can run chopper in a pipe like this:

cat file.fastq | chopper --minlength 1350 --maxlength 1600 --quality 10 > test.fastq

But it seems I cannot run it directly on the file like this:

chopper --minlength 1350 --maxlength 1600 --quality 10  file.fastq> test.fastq

Resulting in:

error: Found argument 'file.fastq' which wasn't expected, or isn't valid in this context

Maybe you could consider adding this functionality to make the use of this tool more straightforward?

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