:fire::bird::fire: PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

Metrics

For full documentation on the pipeline see the Wiki, but quick start instructions are provided below if you are feeling brave.

Quick Start

Install Nextflow (>=21.10.3).

There are several options for install if you do not already have it on your system:
- Install into conda environment, which will require a version of Anaconda to be installed on your system.
```
mamba create -n nextflow -c bioconda nextflow=21.10.6  
```
- If you prefer a to use curl or wget for install see the Nextflow Documentation
Install Docker or Singularity >=3.8.0 for full pipeline reproducibility.
For PHoeNIx >=2.0.0 you will need to download the public Standard-8 version kraken2 database created on or after March 14th, 2023 from Ben Langmead's github page. You CANNOT use an older version of the public kraken databases on Ben Langmead's github page. We thank @BenLangmead and @jenniferlu717 for taking the time to include an extra file in public kraken databases created after March 14th, 2023 to allow them to work in PHoeNIx! You CANNOT use the old database downloaded from CDC’s sharefile. The pipeline is not backwards compatible (hence the bump to version 2).
(optional) If you installed nextflow via a conda environment activate the nextflow environment with:
```
conda activate <environment name>
```

Run PHoeNIx on a test sample loaded with the package with a single command:

nextflow run cdcgov/phoenix -r v2.0.0 -profile <singularity/docker/custom>,test -entry PHOENIX --kraken2db $PATH_TO_DB

Note that this command clones (downloading) the repo to ~/.nextflow/assets/cdcgov/phoenix. See wiki for how to clone and have the software downloaded to a different location.

> * The pipeline comes with config profiles called `docker` and `singularity` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.

Start running your own analysis with a samplesheet!

nextflow run cdcgov/phoenix -r v2.0.0 -profile <singularity/docker/custom> -entry PHOENIX --input <path_to_samplesheet.csv> --kraken2db $PATH_TO_DB

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CDCgov / phoenix

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