From 9e9ff6a86dc80db4c5f3cdd7ddf0bd887c7ff43f Mon Sep 17 00:00:00 2001
From: Oliver Schwengers <oliver@schwengers.de>
Date: Thu, 17 Feb 2022 16:59:31 +0100
Subject: [PATCH] Update Bakta module (#1257)

* bump Bakta version to v1.3.1

* add annotation summary file

* add/amend meta information

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
---
 modules/bakta/main.nf  |  8 +++++---
 modules/bakta/meta.yml | 13 +++++++++----
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/modules/bakta/main.nf b/modules/bakta/main.nf
index 95e87899..a7f971ef 100644
--- a/modules/bakta/main.nf
+++ b/modules/bakta/main.nf
@@ -2,10 +2,10 @@ process BAKTA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
+    conda (params.enable_conda ? "bioconda::bakta=1.3.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -23,6 +23,7 @@ process BAKTA {
     tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
     tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
     tuple val(meta), path("${prefix}.tsv")              , emit: tsv
+    tuple val(meta), path("${prefix}.txt")              , emit: txt
     path "versions.yml"                                 , emit: versions
 
     when:
@@ -61,6 +62,7 @@ process BAKTA {
     touch ${prefix}.hypotheticals.tsv
     touch ${prefix}.hypotheticals.faa
     touch ${prefix}.tsv
+    touch ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bakta/meta.yml b/modules/bakta/meta.yml
index b2bbbf7a..2514a996 100644
--- a/modules/bakta/meta.yml
+++ b/modules/bakta/meta.yml
@@ -1,12 +1,12 @@
 name: bakta
-description: Rapid annotation of bacterial genomes & plasmids.
+description: Annotation of bacterial genomes (isolates, MAGs) and plasmids
 keywords:
   - annotation
   - fasta
-  - prokaryote
+  - bacteria
 tools:
   - bakta:
-      description: Rapid & standardized annotation of bacterial genomes & plasmids.
+      description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
       homepage: https://github.com/oschwengers/bakta
       documentation: https://github.com/oschwengers/bakta
       tool_dev_url: https://github.com/oschwengers/bakta
@@ -29,7 +29,7 @@ input:
         Path to the Bakta database
   - proteins:
       type: file
-      description: FASTA file of trusted proteins to first annotate from (optional)
+      description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
   - prodigal_tf:
       type: file
       description: Training file to use for Prodigal (optional)
@@ -44,6 +44,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - txt:
+      type: file
+      description: genome statistics and annotation summary
+      pattern: "*.txt"
   - tsv:
       type: file
       description: annotations as simple human readble tab separated values
@@ -83,3 +87,4 @@ output:
 
 authors:
   - "@rpetit3"
+  - "@oschwengers"