Research Object Crate for benchAMRking v4.2

This is an aggregation of the work done in [Seq4AMR](https://workflowhub.eu/projects/110) consisting of the following workflows: - [WF1: AbritAMR / AMRFinderPlus](https://workflowhub.eu/workflows/634) - [WF2: Sciensano](https://workflowhub.eu/workflows/644) (**not currently included**) - [WF3: SRST2](https://workflowhub.eu/workflows/407) - [WF4: StarAMR](https://workflowhub.eu/workflows/470) ## Installation - You will need to: - run the RGI Database Builder as a Galaxy admin (if this hasn't been done already) - [Have the en_US.UTF-8 locale installed](https://github.com/galaxyproject/tools-iuc/issues/6467) on the compute nodes executing cast/melt jobs. - Then you can import this workflow - Navigate to `/workflows/import` of your Galaxy server - Select "GA4GH servers" - Enter `name:"benchAMRking"` - And run it - You must provide a Sequencing collection (list:paired of fastq files) - And a Genomes collection (list of fasta files) - Both of these should use **identical** collection element identifiers ## Outputs This will produc

Author

Helena Rasche, Dennis Dollée

License

MIT

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