From dfbb0bc17cb6799892e1d4d2de2f4e08abae92b6 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Thu, 24 Mar 2022 10:49:17 -0600
Subject: [PATCH] update bakta to latest version (v1.4.0) (#1428)

* update bakta to latest version (v1.4.0)

* Update test.yml

* remove empty file md5sums

* bakta was rebuilt to fix dependencies on bioconda

* trigger ci

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 modules/bakta/main.nf        |  6 +++---
 modules/bakta/meta.yml       |  2 +-
 tests/modules/bakta/test.yml | 11 -----------
 3 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/modules/bakta/main.nf b/modules/bakta/main.nf
index a7f971ef..70b2ecdb 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=1.3.1" : null)
+    conda (params.enable_conda ? "bioconda::bakta=1.4.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' :
-        'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
+        'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/bakta/meta.yml b/modules/bakta/meta.yml
index 2514a996..63f55ff3 100644
--- a/modules/bakta/meta.yml
+++ b/modules/bakta/meta.yml
@@ -78,7 +78,7 @@ output:
       pattern: "*.ffn"
   - hypotheticals_tsv:
       type: file
-      description: further information on hypothetical protein CDS as simple human readble tab separated values
+      description: additional information on hypothetical protein CDS as simple human readble tab separated values
       pattern: "*.hypotheticals.tsv"
   - hypotheticals_faa:
       type: file
diff --git a/tests/modules/bakta/test.yml b/tests/modules/bakta/test.yml
index dcfc32bc..1eb3d8a5 100644
--- a/tests/modules/bakta/test.yml
+++ b/tests/modules/bakta/test.yml
@@ -1,25 +1,14 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml bakta
 - name: bakta
   command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run
   tags:
     - bakta
   files:
     - path: output/bakta/test.embl
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.faa
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.ffn
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.fna
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.gbff
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.gff3
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.hypotheticals.tsv
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.hypotheticals.faa
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/bakta/test.tsv
-      md5sum: d41d8cd98f00b204e9800998ecf8427e