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Running a word count on a compressed fastq file now runs wc on the un… #4226

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@dpryan79
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commented Jun 26, 2017

…compressed file

This should fix #4144.

@martenson

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commented Jun 26, 2017

Do I understand it correctly that the issue here is that wc can take 'any' datatype thus won't take advantage of the implicit conversion? If so are there other tools that behave like this?

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commented Jun 26, 2017

Yes, my understanding of #4144 is that it'd be useful to have wc properly handle compressed input. Regarding other data types, the fastq ones are the only ones I know of that stay compressed in Galaxy and don't already have dedicated tools to handle things like this (BAM would be an example of a compressed format for which there are already dedicated tools).

@galaxybot galaxybot added the triage label Jun 26, 2017

@galaxybot galaxybot added this to the 17.09 milestone Jun 26, 2017


##Handle compressed (fastq) input
#if $input1.is_of_type("fastq.gz"):
zcat $input1 |

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@nsoranzo

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Single-quote $input1 here and below?

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@dpryan79

dpryan79 Jun 26, 2017

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Yes, thanks for catching this!

@nsoranzo nsoranzo merged commit ce1316d into galaxyproject:dev Jun 26, 2017

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commented Jun 26, 2017

Thanks @dpryan79!

@bgruening

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commented Jun 26, 2017

Nice! :)

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commented Jun 26, 2017

@dpryan79 my question was whether there are more wc-like tools that will take fastq.gz and do unreasonable things instead of decompressing it

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commented Jun 26, 2017

@martenson Ah, probably? wc is the only one I know of that people are likely to use though.

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