From af842a62b15b8d9ccbde9e74daee571ef6110968 Mon Sep 17 00:00:00 2001
From: Daniel-VM <danielvmillares@gmail.com>
Date: Thu, 26 Oct 2023 14:31:23 +0200
Subject: [PATCH] update bakta to v1.8.2

---
 modules.json                                  |  5 ++---
 .../bakta-baktadbdownload.diff                | 19 -------------------
 .../bakta/baktadbdownload/environment.yml     |  6 ++++++
 modules/nf-core/bakta/baktadbdownload/main.nf |  6 +++---
 .../nf-core/bakta/baktadbdownload/meta.yml    |  5 +++--
 5 files changed, 14 insertions(+), 27 deletions(-)
 delete mode 100644 modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
 create mode 100644 modules/nf-core/bakta/baktadbdownload/environment.yml

diff --git a/modules.json b/modules.json
index 87f35378..1eda682c 100644
--- a/modules.json
+++ b/modules.json
@@ -12,9 +12,8 @@
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff"
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "installed_by": ["modules"]
                     },
                     "canu": {
                         "branch": "master",
diff --git a/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff b/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
deleted file mode 100644
index 7e2459d7..00000000
--- a/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
+++ /dev/null
@@ -1,19 +0,0 @@
-Changes in module 'nf-core/bakta/baktadbdownload'
---- modules/nf-core/bakta/baktadbdownload/main.nf
-+++ modules/nf-core/bakta/baktadbdownload/main.nf
-@@ -1,10 +1,10 @@
- process BAKTA_BAKTADBDOWNLOAD {
-     label 'process_single'
- 
--    conda "bioconda::bakta=1.8.2"
-+    conda "bioconda::bakta=1.8.1"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
--        'biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
-+        'https://depot.galaxyproject.org/singularity/bakta:1.8.1--pyhdfd78af_0' :
-+        'biocontainers/bakta:1.8.1--pyhdfd78af_0' }"
- 
-     output:
-     path "db*"              , emit: db
-
-************************************************************
diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml
new file mode 100644
index 00000000..102348df
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bakta=1.8.2
diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
index 5cf0bbb3..4c111045 100644
--- a/modules/nf-core/bakta/baktadbdownload/main.nf
+++ b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -1,10 +1,10 @@
 process BAKTA_BAKTADBDOWNLOAD {
     label 'process_single'
 
-    conda "bioconda::bakta=1.8.1"
+    conda 'modules/nf-core/bakta/baktadbdownload/environment.yml'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.8.1--pyhdfd78af_0' :
-        'biocontainers/bakta:1.8.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
+        'biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
 
     output:
     path "db*"              , emit: db
diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml
index 996f5b0c..21acacda 100644
--- a/modules/nf-core/bakta/baktadbdownload/meta.yml
+++ b/modules/nf-core/bakta/baktadbdownload/meta.yml
@@ -15,7 +15,6 @@ tools:
       tool_dev_url: https://github.com/oschwengers/bakta
       doi: "10.1099/mgen.0.000685"
       licence: ["GPL v3"]
-
 output:
   - versions:
       type: file
@@ -25,7 +24,9 @@ output:
       type: directory
       description: BAKTA database directory
       pattern: "db*/"
-
 authors:
   - "@jfy133"
   - "@jasmezz"
+maintainers:
+  - "@jfy133"
+  - "@jasmezz"