Merge pull request #138 from nf-core/tool-versions

Update tool versions

Author: nictru

conf/test.config

@@ -23,6 +23,15 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input            = params.pipelines_testdata_base_path + 'scdownstream/samplesheet.csv'
-    integration_hvgs = 500
+    input               = params.pipelines_testdata_base_path + 'scdownstream/samplesheet.csv'
+    integration_methods = 'scvi,harmony,bbknn,combat'
+    doublet_detection   = 'solo,scrublet,doubletdetection,scds'
+    celltypist_model    = 'Adult_Human_Skin'
+    integration_hvgs    = 500
+}
+
+process {
+    withName: SCVITOOLS_SOLO {
+        ext.max_epochs = 5
+    }
 }

modules/local/adata/barcodes/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::anndata=0.10.7
+  - conda-forge::anndata=0.11.1

modules/local/adata/barcodes/main.nf

@@ -4,8 +4,8 @@ process ADATA_BARCODES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata:0.10.7--e9840a94592528c8':
-        'community.wave.seqera.io/library/anndata:0.10.7--336c6c1921a0632b' }"
+        'oras://community.wave.seqera.io/library/anndata:0.11.1--426fb199a9be8838':
+        'community.wave.seqera.io/library/anndata:0.11.1--75463acd25743929' }"
 
     input:
     tuple val(meta), path(h5ad), path(barcodes_csv)

modules/local/adata/extend/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::anndata=0.10.7
+  - conda-forge::anndata=0.11.1

modules/local/adata/extend/main.nf

@@ -4,8 +4,8 @@ process ADATA_EXTEND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata:0.10.7--e9840a94592528c8':
-        'community.wave.seqera.io/library/anndata:0.10.7--336c6c1921a0632b' }"
+        'oras://community.wave.seqera.io/library/anndata:0.11.1--426fb199a9be8838':
+        'community.wave.seqera.io/library/anndata:0.11.1--75463acd25743929' }"
 
     input:
     tuple val(meta), path(base)

modules/local/adata/getsize/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::anndata=0.10.7
+  - conda-forge::anndata=0.11.1

modules/local/adata/getsize/main.nf

@@ -4,8 +4,8 @@ process ADATA_GETSIZE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata:0.10.7--e9840a94592528c8':
-        'community.wave.seqera.io/library/anndata:0.10.7--336c6c1921a0632b' }"
+        'oras://community.wave.seqera.io/library/anndata:0.11.1--426fb199a9be8838':
+        'community.wave.seqera.io/library/anndata:0.11.1--75463acd25743929' }"
 
     input:
     tuple val(meta), path(h5ad)

modules/local/adata/merge/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::scanpy=1.10.1
+  - conda-forge::scanpy=1.10.4

modules/local/adata/merge/main.nf

@@ -5,8 +5,8 @@ process ADATA_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/scanpy:1.10.1--ea08051addf267ac':
-        'community.wave.seqera.io/library/scanpy:1.10.1--0c8c97148fc05558' }"
+        'oras://community.wave.seqera.io/library/scanpy:1.10.4--c2d474f46255931c':
+        'community.wave.seqera.io/library/scanpy:1.10.4--f905699eb17b6536' }"
 
     input:
     tuple val(meta),  path(h5ads)

modules/local/adata/mergeembeddings/environment.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::scanpy=1.10.1
+  - conda-forge::scanpy=1.10.4