🔥🐦🔥 PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

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 Documentaiton
Install Docker or Singularity >=3.8.0 for full pipeline reproducibility.
Email HAISeq@cdc.gov, with the subject line "krakenDB invite request" to request access to the sharefile link and provide the email address to send invite to.
Download the hash.k2d, opts.k2d, and taxo.k2d files needed for the kraken2 subworkflow of PHoeNIx from the CDC sharefile link. You CANNOT use a different krakenDB for this as it needs to match the ktax_map.k2 file that is included in the pipeline. At this time this is not downloadable via command line. Once downloaded the folder containing these files is passed to PHoeNIx via the --kraken2db.

If you ran the v1.0.0-dev version of the pipeline and already downloaded the hash.k2d file there is no need to redownload it. The opts.k2d, and taxo.k2d are found in the phoenix/assets/databases folder. You can just copy these over into a new folder to pass to the PHoeNIx.
(optional) If you installed nextflow via a conda environment activate the nextflow environment with:

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

nextflow run cdcgov/phoenix -r v1.0.0 -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 v1.0.0 -profile <singularity/docker/custom> -entry PHOENIX --input <path_to_samplesheet.csv> --kraken2db $PATH_TO_DB

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hseabolt/phoenix