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microgenlab / porefile

A Nextflow full-length 16S profiling pipeline for ONT reads
GNU General Public License v3.0
22 stars 4 forks source link

This is cool! #10

Closed KFeye closed 3 years ago

KFeye commented 3 years ago

Hello!

So, I am slightly obsessed with the idea of this analysis tool, so I apologize if I ask too many questions. I am trying to run the program (MacOS) and I have been using the barcode kit (96 expansion) and am trying very hard to get to a spot where I have taxa bar plots and diversity analysis.

I demultiplexed and trimmed in guppy. I have 96 folders with fastq.gz files (multiple per barcode). How would I read that data in and do I need to pre-process it any other way (so unzip everything and put it in one fast.gz file?? Also, does it make sense to go to google cloud? Is there a metadata file I need to create?

This is truly great work. Thank you!

iferres commented 3 years ago

Hi @KFeye, thanks for your words haha. Very funny the "obsessed" part. We are glad you find it useful.

Idk your experience with nextflow and docker/singularity, but the pipeline should work on your data. Are you having any problem with that?

May be use --fq */*.fastq.gz to grab files within sub-folders, that should work.

If it's already demultiplexed, pass the --isDemultiplexed to avoid running Porechop. The pipeline will consider each file as a different barcode and will process them separately.

There's also an issue with the conda version of Nanoplot, which makes the pipeline fail. Use --noNanoplot if that happens.