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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
469 stars 151 forks source link

passing arguments to cutadapt #13

Closed samuelCollombet closed 6 years ago

samuelCollombet commented 6 years ago

Hi, Sorry if this is not the best place to write that... It seems that there is no possibility in Trim_galore to pass arguments to cutapadt, am I right? Would it be possible to add this option? The main reason I am asking that is because the latest version of cutadapt as an option to be multi-threaded, and it would be great to be able to use it when using trim_galore to speed up a bit the process :)

Many thanks!

FelixKrueger commented 6 years ago

Hi Samuel, This has actually been asked last week already, but I believe this would probably be a fairly major rewrite. I might reconsider if the multicore option becomes a more permanent feature of Cutadapt. Please also see here: https://github.com/FelixKrueger/TrimGalore/issues/12

samuelCollombet commented 6 years ago

Oops sorry I didn't check closed issues. Thanks for the answer! Would be a great feature, let's see how it goes with cutadapt :) Best, samuel

On 11 December 2017 at 17:25, FelixKrueger notifications@github.com wrote:

Hi Samuel, This has actually been asked last week already, but I believe this would probably be a fairly major rewrite. I might reconsider if the multicore option becomes a more permanent feature of Cutadapt. Please also see here:

12 https://github.com/FelixKrueger/TrimGalore/issues/12

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/FelixKrueger/TrimGalore/issues/13#issuecomment-350776014, or mute the thread https://github.com/notifications/unsubscribe-auth/ARoG2SeZfo6rlyZsPbe4_n497MlhrzSYks5s_VdugaJpZM4Q9pxP .