adding option --skip_demultiplexing

[nbargues]

Hi, I try to test your pipeline and it seems to work well. But with new version of Nanopore software, file are always already demultiplex (fastq.gz). Can you add a --skip_demultiplexing argument ? Or indicate me what to change in your script because i did not find by myself.

Regards

[MaestSi]

Hi, if you are doing live basecalling and demultiplexing, now embedded in MinKNOW, and have performed quality filtering, adapters and PCR primers trimming, so that you already have a BC\<num>.fastq.gz, you could run the pipeline using the following command:

source activate MetONTIIME_env
nohup ./MetONTIIME.sh <working_dir> <metadata file> <sequences qiime2 artifact> <taxonomy qiime2 artifact> <threads> <taxonomic classifier> &

where:

<working_dir>: directory containing fastq.gz files
<metadata file>: full path to metadata file; if the file doesn't exist yet, it is created by the pipeline
<sequences qiime2 artifact>: <file name>_sequence.qza QIIME2 artifact, may be created by Import_database.sh script
<taxonomy qiime2 artifact>: <file name>_taxonomy.qza QIIME2 artifact, may be created by Import_database.sh script
<threads>: maximum number of threads used
<taxonomic classifier>: either Blast or Vsearch; Vsearch option was created due to a user's request, since it is multithreaded, but it revealed to be way slower than Blast. I'd go for Blast.

Let me know if this is what you had in mind and if it works as expected! Simone

[nbargues]

Thanks for the quick answer. I will try your command soon and come back for feedback.

Cheers

[MaestSi]

Hi, I have tested the command myself, and it worked. I also added a section for this in the README. If you confirm that it worked also for you, I am going to close the issue. Simone