error: Found argument 'file.fastq' which wasn't expected, or isn't valid in this context about chopper HOT 8 CLOSED

It seems like you are reinventing a workflow system like snakemake. Maybe that solves the needs that you try to take care of in your python code.

I can also recommend the python shlex module, which you could use to avoid splitting the arguments in a list:

import shlex
cmd_chopper = shlex.split('chopper -l 1 -q 3 --headcrop 30 --tailcrop 30 --threads 12')

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Hi,

Yes, that would be possible, I will put your request on the list :-)

Wouter

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Oh, that would be great! :)

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Any progress on this? :)

I can't implement chopper in my pipeline. I've tried piping with subprocess.Popen, but get the same error.

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I can't implement chopper in my pipeline. I've tried piping with subprocess.Popen, but get the same error.

That should work, in principle. Which (python?) code leads to that error?

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My bad. I found a mistake in my code.

It seems to work doing this:

input1 = 'barcode37.fastq'
cmd_cat = ['cat', input1]
fastq = subprocess.Popen(cmd_cat, stdout=subprocess.PIPE)


cmd_chopper = ['chopper', '-l', '1','-q', '3','--headcrop', '30', '--tailcrop', '30', '--threads', '12']

reads_trim = open('test.fastq', 'w')
chopper = subprocess.Popen(cmd_chopper, stdin=fastq.stdout, stdout=reads_trim)

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

@wdecoster Any update of this issue? I also found this enhancement to be very useful. But the latest chopper 0.7.0 still do not have the feature.
If you agree, I would be happy to implement this feature and make a PR.

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Implemented thanks to @JMencius! I will make a new release soon.

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