Replies: 4 comments 19 replies
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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 If it's already demultiplexed, pass the There's also an issue with the conda version of Nanoplot, which makes the pipeline fail. Use |
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Since this wasn't a bug report, I moved the issue here to discussions to follow the conversation. |
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Thanks! I tried to move it...but failed.
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On Mar 16, 2021, at 3:53 PM, Ignacio Ferrés ***@***.***> wrote:
Since this wasn't a bug report, I moved the issue here to discussions to follow the conversation.
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Hey!
My background is working with QIIME2, doing some python work in conda, and
moving files around (so super light). I also do some work in R (phyloseq,
ggplot2, stats...)
The command line I am running is$ nextflow run microgenlab/porefile --fq
'FASTQFilesZinpro2/' --minimap2 --isDemultiplexed
N E X T F L O W ~ version 20.10.0
I ran the sample data for Nextflow through their pipeline for a BLAST
(found on their site) and was successful.
I have docker and conda, I have everything updated completely.
…On Thu, Mar 18, 2021 at 11:40 AM Ignacio Ferrés ***@***.***> wrote:
Also, I'd like to know what's your background using the command line. Just
to know the level of detail you may need to understand the commands.
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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!
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