From d71fc8b7e58e0b6409fc5a0745464fb41288d84d Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Mon, 22 Jul 2024 10:59:33 -0300
Subject: [PATCH] chore: Update bakta db download version

---
 .../bakta-baktadbdownload.diff                | 14 +++++
 .../bakta/baktadbdownload/environment.yml     |  7 +++
 modules/nf-core/bakta/baktadbdownload/main.nf |  4 +-
 .../nf-core/bakta/baktadbdownload/meta.yml    |  5 +-
 .../bakta/baktadbdownload/tests/main.nf.test  | 55 +++++++++++++++++++
 .../baktadbdownload/tests/main.nf.test.snap   | 29 ++++++++++
 .../baktadbdownload/tests/nextflow.config     |  7 +++
 .../bakta/baktadbdownload/tests/tags.yml      |  2 +
 8 files changed, 119 insertions(+), 4 deletions(-)
 create mode 100644 modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
 create mode 100644 modules/nf-core/bakta/baktadbdownload/environment.yml
 create mode 100644 modules/nf-core/bakta/baktadbdownload/tests/main.nf.test
 create mode 100644 modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/bakta/baktadbdownload/tests/nextflow.config
 create mode 100644 modules/nf-core/bakta/baktadbdownload/tests/tags.yml

diff --git a/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff b/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
new file mode 100644
index 00000000..cd309e33
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/bakta-baktadbdownload.diff
@@ -0,0 +1,14 @@
+Changes in module 'nf-core/bakta/baktadbdownload'
+--- modules/nf-core/bakta/baktadbdownload/main.nf
++++ modules/nf-core/bakta/baktadbdownload/main.nf
+@@ -4,7 +4,7 @@
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+         'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' :
+-        'biocontainers/bakta:1.9.3--pyhdfd78af_0' }"
++        'quay.io/biocontainers/bakta:1.7.0--pyhdfd78af_1' }"
+ 
+     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..f6a53ff7
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/environment.yml
@@ -0,0 +1,7 @@
+name: bakta_baktadbdownload
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bakta=1.9.3
diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
index f5e6d111..27c6b6aa 100644
--- a/modules/nf-core/bakta/baktadbdownload/main.nf
+++ b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -1,9 +1,9 @@
 process BAKTA_BAKTADBDOWNLOAD {
     label 'process_single'
 
-    conda "bioconda::bakta=1.7.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' :
+        'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' :
         'quay.io/biocontainers/bakta:1.7.0--pyhdfd78af_1' }"
 
     output:
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"
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test
new file mode 100644
index 00000000..a5f827f9
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test
@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process BAKTA_BAKTADBDOWNLOAD"
+    script "../main.nf"
+    process "BAKTA_BAKTADBDOWNLOAD"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bakta"
+    tag "bakta/baktadbdownload"
+
+    test("Bakta database download") {
+
+        when {
+            process {
+                """
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.db.get(0)).exists() },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+    test("Bakta database download - stub") {
+    
+        options "-stub"
+
+        when {
+            process {
+                """
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.db + 
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
new file mode 100644
index 00000000..b1c82267
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
@@ -0,0 +1,29 @@
+{
+    "Bakta database download": {
+        "content": [
+            [
+                "versions.yml:md5,df9b091b08a41b7d5eef95727b7eac29"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T11:34:41.812416438"
+    },
+    "Bakta database download - stub": {
+        "content": [
+            [
+                [
+                    
+                ],
+                "versions.yml:md5,df9b091b08a41b7d5eef95727b7eac29"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T11:35:01.082923401"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/nextflow.config b/modules/nf-core/bakta/baktadbdownload/tests/nextflow.config
new file mode 100644
index 00000000..8b99646a
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: 'BAKTA_BAKTADBDOWNLOAD' {
+        ext.args = "--type light"
+    }
+
+}
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/tags.yml b/modules/nf-core/bakta/baktadbdownload/tests/tags.yml
new file mode 100644
index 00000000..c469fa48
--- /dev/null
+++ b/modules/nf-core/bakta/baktadbdownload/tests/tags.yml
@@ -0,0 +1,2 @@
+bakta/baktadbdownload:
+  - "modules/nf-core/bakta/baktadbdownload/**"