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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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Add ability to join paired reads #12

Closed johnchase closed 7 years ago

johnchase commented 7 years ago

Similar to running dada2 in R it would be nice to have the ability to join paired reads with the q2 plugin

benjjneb commented 7 years ago

Is there currently a QIIME object for paired fastq files (or lists of paired fastq files)?

johnchase commented 7 years ago

I don't believe that there is. @ebolyen can you confirm?

ebolyen commented 7 years ago

There is if I understand the question correctly: SampleData[PairedEndSequencesWithQuality] which uses SingleLanePerSamplePairedEndFastqDirFmt as its backing directory format.

benjjneb commented 7 years ago

If that exists already, then adding a paired end workflow should be straightforward.

Is there documentation of SampleData[PairedEndSequencesWithQuality] objects? For example, can it be assumed there are always forward and reverse files for each sample?

ebolyen commented 7 years ago

No real documentation, and we can't yet enforce that there exists a forward and reverse for each sample, but I believe it is our goal to be able to validate that property. That particular directory format does contain a manifest file which maps the sample id to the filepath and direction.

relevant lines for format manifest definition q2-demux which manipulates these

These parts of the API (multi-file directory formats) are still very rough around the edges, but we're thinking about ways to make it easier.

benjjneb commented 7 years ago

Added in a1857e54ef0599e956c2f73bed1b0bc6851ac946 and b66432da308a924a26f315a517c934b4a335af2f

Assumes dada2 1.2+