Big Bakta update

CHANGELOG.md

@@ -7,12 +7,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#235](https://github.com/nf-core/funcscan/pull/235) Added parameter `annotation_bakta_db_downloadtype` to be able to switch between downloading either full (33.1 GB) or light (1.3 GB excluding UPS, IPS, PSC, see parameter description) versions of the Bakta database. (by @jasmezz)
+
 ### `Fixed`
 
 - [#237](https://github.com/nf-core/funcscan/pull/237) Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
+- [#235](https://github.com/nf-core/funcscan/pull/235) Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
+- [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
 
 ### `Dependencies`
 
+| Tool  | Previous version | New version |
+| ----- | ---------------- | ----------- |
+| Bakta | 1.6.1            | 1.7.0       |
+
 ### `Deprecated`
 
 ## v1.0.1 - [2023-02-27]

conf/modules.config

@@ -91,6 +91,9 @@ process {
             enabled: params.save_databases,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.args = [
+            "--type ${params.annotation_bakta_db_downloadtype}"
+        ].join(' ').trim()
     }
 
     withName: BAKTA_BAKTA {
@@ -107,17 +110,18 @@ process {
             params.annotation_bakta_complete ? '--complete' : '',
             params.annotation_bakta_renamecontigheaders ? '' : '--keep-contig-headers',
             params.annotation_bakta_compliant ? '--compliant' : '',
-            params.annotation_bakta_skiptrna ? '--skip-trna' : '',
-            params.annotation_bakta_skiptmrna ? '--skip-tmrna' : '',
-            params.annotation_bakta_skiprrna ? '--skip-rrna' : '',
-            params.annotation_bakta_skipncrna ? '--skip-ncrna' : '',
-            params.annotation_bakta_skipncrnaregion ? '--skip-ncrna-region' : '',
-            params.annotation_bakta_skipcrispr ? '--skip-crispr' : '',
+            params.annotation_bakta_trna ? '' : '--skip-trna',
+            params.annotation_bakta_tmrna ? '' : '--skip-tmrna',
+            params.annotation_bakta_rrna ? '' : '--skip-rrna',
+            params.annotation_bakta_ncrna ? '' : '--skip-ncrna',
+            params.annotation_bakta_ncrnaregion ? '' : '--skip-ncrna-region',
+            params.annotation_bakta_crispr ? '' : '--skip-crispr',
             params.annotation_bakta_skipcds ? '--skip-cds' : '',
-            params.annotation_bakta_skippseudo ? '--skip-pseudo' : '',
+            params.annotation_bakta_pseudo ? '' : '--skip-pseudo',
             params.annotation_bakta_skipsorf ? '--skip-sorf' : '',
-            params.annotation_bakta_skipgap ? '--skip-gap' : '',
-            params.annotation_bakta_skipori ? '--skip-ori' : ''
+            params.annotation_bakta_gap ? '' : '--skip-gap',
+            params.annotation_bakta_ori ? '' : '--skip-ori',
+            params.annotation_bakta_activate_plot ? '' : '--skip-plot'
         ].join(' ').trim()
     }
 

docs/usage.md

@@ -100,7 +100,7 @@ As a reference, we will describe below where and how you can obtain databases an
 
 nf-core/funcscan offers multiple tools for annotating input sequences. Bakta is a new tool touted as a bacteria-only successor to the well-established Prokka.
 
-To supply the required Bakta database (and not have the pipeline do that at every new run), use the flag `--annotation_bakta_db`. It must be downloaded from the Bakta Zenodo archive, the link of which can be found on the [Bakta GitHub repository](https://github.com/oschwengers/bakta#database-download).
+To supply the preferred Bakta database (and not have the pipeline download at every new run), use the flag `--annotation_bakta_db_localpath`. The full or light Bakta database must be downloaded from the Bakta Zenodo archive, the link of which can be found on the [Bakta GitHub repository](https://github.com/oschwengers/bakta#database-download).
 
 Once downloaded this must be untarred:
 
@@ -111,7 +111,7 @@ tar xvzf db.tar.gz
 And then passed to the pipeline with:
 
 ```bash
---annotation_bakta_db /<path>/<to>/db/
+--annotation_bakta_db_localpath /<path>/<to>/db/
 ```
 
 > ℹ️ The flag `--save_databases` saves the pipeline-downloaded databases in your results directory. You can then move these to a central cache directory of your choice for re-use in the future.

modules.json

@@ -47,12 +47,12 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "eeb194e70c5acc713891a9eb21fdd397cca9dff8",
+                        "git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "ade45f05a2659b5c130a483e09f50b7f33d075b2",
+                        "git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
                         "installed_by": ["modules"]
                     },
                     "bioawk": {

nextflow.config

@@ -26,24 +26,26 @@ params {
     annotation_prodigal_transtable          = 11
     annotation_prodigal_forcenonsd          = false
 
-    annotation_bakta_db                     = null
+    annotation_bakta_db_localpath           = null
+    annotation_bakta_db_downloadtype        = 'full'
     annotation_bakta_mincontiglen           = 1
     annotation_bakta_translationtable       = 11
     annotation_bakta_gram                   = '?'
     annotation_bakta_complete               = false
     annotation_bakta_renamecontigheaders    = false
     annotation_bakta_compliant              = false
-    annotation_bakta_skiptrna               = false
-    annotation_bakta_skiptmrna              = false
-    annotation_bakta_skiprrna               = false
-    annotation_bakta_skipncrna              = false
-    annotation_bakta_skipncrnaregion        = false
-    annotation_bakta_skipcrispr             = false
+    annotation_bakta_trna                   = false
+    annotation_bakta_tmrna                  = false
+    annotation_bakta_rrna                   = false
+    annotation_bakta_ncrna                  = false
+    annotation_bakta_ncrnaregion            = false
+    annotation_bakta_crispr                 = false
     annotation_bakta_skipcds                = false
-    annotation_bakta_skippseudo             = false
+    annotation_bakta_pseudo                 = false
     annotation_bakta_skipsorf               = false
-    annotation_bakta_skipgap                = false
-    annotation_bakta_skipori                = false
+    annotation_bakta_gap                    = false
+    annotation_bakta_ori                    = false
+    annotation_bakta_activate_plot          = false
 
     annotation_prokka_singlemode            = false
     annotation_prokka_rawproduct            = false