# Real-time analysis with the EPI2ME wf-metagenomics workflow

# Link https://bit.ly/NGS_RT

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Tomorrow you will get some more background information and additionally run the pipeline on the full dataset generated from the nanopore sequencing.

Today we will run the workflow in real-time as the reads are being generated. This is thanks to certain functions in the Nextflow workflow language. See this article for a more detailed discussion if desired: https://labs.epi2me.io/progressive-kraken2/

### Instructions to run the workflow in real-time:

1) If you are running on MacOS, Make sure the Docker application is open and running
2) Within the home directory, ```Users/onp/``` Make a directory to run the analysis and change into it:

mkdir RealTime_TaxClass

cd RealTime_TaxClass

3) Run the following command ensuring all paths point to the appropriate files:

nextflow run tslaird/wf-metagenomics --fastq {path/to/fastq/directory} \
--out_dir RealTime_output_k2_standard_08gb/ \
--database /Users/onp/databases/k2_standard_08gb \
--amr --amr_db resfinder \
--real_time \
--batch_size 500

Once initiated it may take a little while for the results to be generated. When a batch has been processed the report will appear in the output folder as:

You can click on that link to open it in a browser window.

As new batches of fastq files get classified the report will update. You can update the report by refreshing the webpage it is loaded in.


### Further reading
To better familiarize yourself with the workflow you can read about it here: https://github.com/epi2me-labs/wf-metagenomics