Add new module for gene annotation: Bakta

CHANGELOG.md

@@ -3,7 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.1.1dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/11
+## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/19
+
+This version implements Bakta for gene annotaton and updates the MultiQC module.
+
+### `Added`
+
+- [#95](https://github.com/nf-core/bacass/pull/95) - Subworkflow for gene annotation with Bakta
+- [#95](https://github.com/nf-core/bacass/pull/95) - Update MultiQC module to v1.17
+
+## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/11
 
 Enhancement of the MultiQC report.
 

README.md

@@ -38,7 +38,7 @@ For users specifying both short read and long read (NanoPore) data, the pipeline
 
 ### Assembly QC and annotation
 
-In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quast). The resulting bacterial assembly is furthermore annotated using [Prokka](https://github.com/tseemann/prokka) or [DFAST](https://github.com/nigyta/dfast_core).
+In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quast). The resulting bacterial assembly is furthermore annotated using [Prokka](https://github.com/tseemann/prokka), [Bakta](https://github.com/oschwengers/bakta) or [DFAST](https://github.com/nigyta/dfast_core).
 
 ## Usage
 

conf/modules.config

@@ -249,3 +249,23 @@ if (!params.skip_fastp) {
         }
     }
 }
+
+if (params.annotation_tool == 'bakta') {
+    if (params.baktadb_download == true) {
+        process {
+            withName: '.*:.*:BAKTA_DBDOWNLOAD_RUN:BAKTA_BAKTADBDOWNLOAD' {
+                ext.args = params.baktadb_download_args ? params.baktadb_download_args : ''
+            }
+        }
+    }
+    process {
+        withName: '.*:.*:BAKTA_DBDOWNLOAD_RUN:BAKTA_BAKTA' {
+            ext.args    = ''
+            publishDir  = [
+                path: { "${params.outdir}/Bakta/${meta.id}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+}

docs/output.md

@@ -190,7 +190,7 @@ The assembly QC is performed with [QUAST](http://quast.sourceforge.net/quast) fo
 
 ## Annotation
 
-By default, the assembly is annotated with [Prokka](https://github.com/tseemann/prokka) which acts as frontend for several annotation tools and includes rRNA and ORF predictions. Alternatively, on request, the assembly is annotated with [DFAST](https://github.com/nigyta/dfast_core).
+By default, the assembly is annotated with [Prokka](https://github.com/tseemann/prokka) which acts as frontend for several annotation tools and includes rRNA and ORF predictions. Alternatively, on request, the assembly is annotated with [Bakta](https://github.com/oschwengers/bakta) or [DFAST](https://github.com/nigyta/dfast_core).
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -204,6 +204,13 @@ See [Prokka's documentation](https://github.com/tseemann/prokka#output-files) fo
 
 ![Prokka annotation](images/prokka.png)
 
+- `Bakta/{ID}/`
+  - `*.gff3`: Annotations in gff3 format
+  - `*.txt`: Summary in txt format
+  - `*.faa`: CDS/sORF amino acid sequences in fasta format
+
+See [Baktas's documentation](https://github.com/oschwengers/bakta#output) for a full description of all output files.
+
 - `DFAST/{ID}_results/`
   - `genome.gff`: Annotation in gff format
   - `statistics.txt`: Annotation statistics in text format

modules.json

@@ -5,6 +5,17 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bakta/bakta": {
+                        "branch": "master",
+                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
+                        "installed_by": ["modules"]
+                    },
+                    "bakta/baktadbdownload": {
+                        "branch": "master",
+                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff"
+                    },
                     "canu": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -47,7 +58,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
+                        "git_sha": "c4e79dd48ab2cedea2d7d525582bea061c241e0f",
                         "installed_by": ["modules"]
                     },
                     "nanoplot": {
@@ -85,6 +96,11 @@
                         "branch": "master",
                         "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["modules"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "installed_by": ["modules"]
                     }
                 }
             },