Expose --m (min output read length) parameter

Question

Expose --m (min output read length) parameter

thermokarst opened this issue 7 years ago · comments

Matthew Ryan Dillon commented 7 years ago

For now reads that don't pass this filter will have to be written to /dev/null, since we haven't squared away the nullable outputs situation brought up in #10. In the meantime, the methods can use a Range to enforce a minimum read length of 1, which will prevent FastqGzFormat validation issues.

This recently came up on the forum:

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edisagarcia · Answer 1 · Wed Jun 13 2018 17:02:23 GMT+0800 (China Standard Time)

Hi thermokarst,
Please can you explain the use of Range in the qiime cutadapt demuxed -paired command? (QIIME2 2018)
I also have the problem with the FastqGzFormat recognition.
Please HELP!!

Matthew Ryan Dillon · Answer 2 · Wed Jun 13 2018 20:26:25 GMT+0800 (China Standard Time)

Hi there @edisagarcia, sorry to hear things aren't going well. Can you ask for help over at https://forum.qiime2.org? That is where we provide general user support for QIIME 2. Thanks!

Matthew Ryan Dillon · Answer 3 · Tue May 14 2019 12:13:35 GMT+0800 (China Standard Time)

Whoops! Forgot to implement this for demux_single and demux_paired. @Oddant1, you up for taking that on? You can take the work that was done in #28 and apply it to the two demux methods. If you're up for it, let's chat Tuesday or Wednesday. Thanks!

Anthony Simard · Answer 4 · Tue May 14 2019 23:42:39 GMT+0800 (China Standard Time)

@thermokarst that sounds great, I'm looking over it right now.