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@@ -10,7 +10,7 @@ The output of nf-core/funcscan provides reports for each of the functional group
As a general workflow, we recommend to first look at the summary reports ([ARGs](#hamronization), [AMPs](#ampcombi), [BGCs](#combgc)), to get a general overview of what hits have been found across all the tools of each functional group. After which, you can explore the specific output directories of each tool to get more detailed information about each result. The tool-specific output directories also includes the output from the functional annotation steps of either [prokka](https://github.com/tseemann/prokka), [pyrodigal](https://github.com/althonos/pyrodigal), [prodigal](https://github.com/hyattpd/Prodigal), or [Bakta](https://github.com/oschwengers/bakta) if the `--save_annotations` flag was set.
Similarly, all downloaded databases are saved (i.e. from [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), and/or [AMPcombi](https://github.com/Darcy220606/AMPcombi)) into the output directory `<outdir>/downloads/` if the `--save_databases` flag was set.
Similarly, all downloaded databases are saved (i.e. from [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [AMPcombi](https://github.com/Darcy220606/AMPcombi), and [RGI](https://github.com/arpcard/rgi)) into the output directory `<outdir>/databases/` if the `--save_databases` flag was set.
Furthermore, for reproducibility, versions of all software used in the run is presented in a [MultiQC](http://multiqc.info) report.
