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nf-core · Dec 12, 2024 · cd0495b · cd0495b
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commit cd0495b
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Showing 7 changed files with 26 additions and 25 deletions.
diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
@@ -24,7 +24,9 @@ process BUSCO_BUSCO {
     tuple val(meta), path("*-busco/*/run_*/busco_sequences")          , emit: seq_dir               , optional: true
     tuple val(meta), path("*-busco/*/translated_proteins")            , emit: translated_dir        , optional: true
     tuple val(meta), path("*-busco")                                  , emit: busco_dir
-    tuple val(meta), path("busco_downloads")                          , emit: busco_downloads_dir   , optional: true
+    tuple val(meta), path("busco_downloads/lineages/*")               , emit: downloaded_lineages   , optional: true
+        tuple val(meta), path("busco_downloads/lineages/*")               , emit: downloaded_lineages   , optional: true
+
     path "versions.yml"                                               , emit: versions
 
     when:

diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml
@@ -132,16 +132,16 @@ output:
           type: directory
           description: BUSCO lineage specific output
           pattern: "*-busco"
-  - busco_downloads_dir:
+  - busco_downloaded_lineages:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "busco_downloads":
+      - "busco_downloads/lineages/*":
           type: directory
-          description: BUSCO downloads directory
-          pattern: "busco_downloads"
+          description: BUSCO lineages downloaded
+          pattern: "busco_downloads/lineages/*"
   - versions:
       - versions.yml:
           type: file

diff --git a/modules/nf-core/busco/busco/tests/main.nf.test.snap b/modules/nf-core/busco/busco/tests/main.nf.test.snap
@@ -84,7 +84,7 @@
                         ]
                     ]
                 ],
-                "busco_downloads_dir": [
+                "downloaded_lineages": [
 
                 ],
                 "full_table": [
@@ -124,7 +124,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-12T13:52:55.9049764"
+        "timestamp": "2024-12-12T17:53:12.04195472"
     },
     "test_busco_eukaryote_augustus": {
         "content": [

diff --git a/modules/nf-core/busco/generateplot/environment.yml b/modules/nf-core/busco/generateplot/environment.yml
@@ -1,7 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::busco=5.7.1
+  - bioconda::busco=5.8.2
diff --git a/modules/nf-core/busco/generateplot/main.nf b/modules/nf-core/busco/generateplot/main.nf
@@ -3,8 +3,8 @@ process BUSCO_GENERATEPLOT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
-        'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0':
+        'biocontainers/busco:5.8.2--pyhdfd78af_0' }"
 
     input:
     path short_summary_txt, stageAs: 'busco/*'

diff --git a/modules/nf-core/busco/generateplot/tests/main.nf.test.snap b/modules/nf-core/busco/generateplot/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T15:40:01.523993"
+        "timestamp": "2024-12-12T17:44:49.021631034"
     },
     "stub": {
         "content": [
@@ -18,20 +18,20 @@
                     "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "1": [
-                    "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                    "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
                 ],
                 "png": [
                     "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74"
+                    "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-05-03T15:40:11.864276"
+        "timestamp": "2024-12-12T17:44:57.632273743"
     }
 }
diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap
@@ -239,17 +239,17 @@
                 ]
             ],
             [
-                "versions.yml:md5,05d8022e3afb0d5642ed17147b991730",
-                "versions.yml:md5,53987b35fc275297efdaf525937fdca3",
                 "versions.yml:md5,624e4661a636558db4521457fcddf6dd",
                 "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a",
-                "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64"
+                "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64",
+                "versions.yml:md5,ab3572b594228efec5824329cba08997",
+                "versions.yml:md5,b717797e52f95b2e9d5fb139f7c1e8ac"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-11T12:47:41.989229128"
+        "timestamp": "2024-12-12T17:45:57.908942636"
     }
 }