Update scvi-tools version to 1.4.3 (#11648)

* Update scvi-tools version to 1.4.3

* update scvi-tools solo container

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* update scvi-tools solo hash

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* emit versions

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* emit versions

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* lint fix

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* use right hash

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* use right hash

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* use right hash

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* formatting

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* formatting

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

* formatting

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

---------

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

Author: Zethson

modules/nf-core/scvitools/solo/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::scvi-tools=1.3.3
+  - conda-forge::scvi-tools=1.4.3

modules/nf-core/scvitools/solo/main.nf

@@ -4,10 +4,10 @@ process SCVITOOLS_SOLO {
     label 'process_gpu'
 
     conda "${moduleDir}/environment.yml"
-    container "${ task.ext.use_gpu ? 'ghcr.io/scverse/scvi-tools:py3.12-cu12-1.3.3-' :
+    container "${ task.ext.use_gpu ? 'ghcr.io/scverse/scvi-tools:py3.13-cu12-1.4.3-' :
         workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8764e4208e9639a54d636fc65c839c55dedbfd68def57baea90d1d2007d6a7f/data':
-        'community.wave.seqera.io/library/scvi-tools:1.3.3--df115aabdccb7d6b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/df/dfb4b54fd5cb5c5624d947914f5ab8ac86eeaa5f762ebc52c034fbd36cf30250/data':
+        'community.wave.seqera.io/library/scvi-tools:1.4.3--cce8c95b58ececa6' }"
 
     input:
     tuple val(meta), path(h5ad)
@@ -17,7 +17,7 @@ process SCVITOOLS_SOLO {
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
     tuple val(meta), path("*.pkl") , emit: predictions
-    path "versions.yml"            , emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/scvitools/solo/meta.yml

@@ -11,9 +11,9 @@ tools:
       homepage: "https://scvi-tools.org"
       documentation: "https://docs.scvi-tools.org/en/stable/"
       tool_dev_url: "https://github.com/scverse/scvi-tools"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
-
 input:
   - - meta:
         type: map
@@ -55,16 +55,19 @@ output:
           type: file
           description: pandas dataframe containing the doublet classification
           pattern: "*.pkl"
-
           ontologies: []
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
-
         ontologies:
           - edam: http://edamontology.org/format_3750 # YAML
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@LeonHafner"
 maintainers:

modules/nf-core/scvitools/solo/tests/main.nf.test.snap

@@ -2,7 +2,7 @@
     "Should run without batch column": {
         "content": [
             [
-                "versions.yml:md5,6c9c4dfb80bc9f3e68cbf3328f74c6d9"
+                "versions.yml:md5,bb88327d1a949a186e1a243a4ff14ce0"
             ],
             "test.h5ad",
             "test.pkl"
@@ -16,7 +16,7 @@
     "Should run with batch column": {
         "content": [
             [
-                "versions.yml:md5,6c9c4dfb80bc9f3e68cbf3328f74c6d9"
+                "versions.yml:md5,bb88327d1a949a186e1a243a4ff14ce0"
             ],
             "test.h5ad",
             "test.pkl"
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b04fe43d9ea390fc608cb41bbf9136a3"
+                    "versions.yml:md5,c51a5910d7d7235de015822b272544b0"
                 ],
                 "h5ad": [
                     [
@@ -66,7 +66,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b04fe43d9ea390fc608cb41bbf9136a3"
+                    "versions.yml:md5,c51a5910d7d7235de015822b272544b0"
                 ]
             }
         ],