Merge branch 'dev' into update-modules

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#270](https://github.com/nf-core/funcscan/pull/270) Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
 - [#274](https://github.com/nf-core/funcscan/pull/274) Update all modules: changed docker links according to the change of quay.io as default repository. (by @jasmezz)
+- [#275](https://github.com/nf-core/funcscan/pull/275) Save DRAMP database in the common database directory if `--save_databases` is supplied. (by @jasmezz)
 
 ### `Fixed`
 

conf/modules.config

@@ -496,4 +496,13 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: DRAMP_DOWNLOAD {
+        publishDir = [
+            path: { "${params.outdir}/databases/dramp" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_databases,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }

docs/output.md

@@ -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), and/or [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master)) 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), and/or [AMPcombi](https://github.com/Darcy220606/AMPcombi)) into the output directory `<outdir>/downloads/` 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.
 

nextflow_schema.json

@@ -407,7 +407,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-save",
                     "description": "Specify whether to save pipeline-downloaded databases in your results directory.",
-                    "help_text": "While nf-core/funcscan can download databases for you, often these are very large and can significantly slow-down pipeline runtime if the databases have to be downloaded every run.\n\nSpecifying `--save_databases` while save the pipeline-downloaded databases in your results directory. This applies to: BAKTA, DeepBGC, DeepARG, AMRFinderPlus and antiSMASH.\n\nYou can then move the resulting directories/files to a central cache directory of your choice for re-use in the future.\n\nIf you do not specify these flags, the database files will remain in your `work/` directory and will be deleted if `cleanup = true` is specified in your config, or if you run `nextflow clean`.\n"
+                    "help_text": "While nf-core/funcscan can download databases for you, often these are very large and can significantly slow-down pipeline runtime if the databases have to be downloaded every run.\n\nSpecifying `--save_databases` while save the pipeline-downloaded databases in your results directory. This applies to: BAKTA, DeepBGC, DeepARG, AMRFinderPlus, antiSMASH, and DRAMP.\n\nYou can then move the resulting directories/files to a central cache directory of your choice for re-use in the future.\n\nIf you do not specify these flags, the database files will remain in your `work/` directory and will be deleted if `cleanup = true` is specified in your config, or if you run `nextflow clean`.\n"
                 }
             },
             "fa_icon": "fas fa-database"