Add scope to configs (#1013)

* Add scope to configs

* Fix some scope

* Fix double scope keys

* Remove some more duplicate scopes

* Adjust the scope of some components and workflows

* Add CHANGELOG entry

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

Author: DriesSchaumont

CHANGELOG.md

@@ -1,5 +1,6 @@
 name: celltypist
 namespace: annotate
+scope: "public"
 description: Automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm.
 authors:
   - __merge__: /src/authors/jakub_majercik.yaml

src/annotate/celltypist/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: onclass
 namespace: annotate
+scope: "public"
 description: |
   OnClass is a python package for single-cell cell type annotation. It uses the Cell Ontology to capture the cell type similarity. 
   These similarities enable OnClass to annotate cell types that are never seen in the training data.

src/annotate/onclass/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: popv
 namespace: "annotate"
+scope: "public"
 description: "Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV."
 authors:
   - __merge__: /src/authors/matthias_beyens.yaml

src/annotate/popv/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: random_forest_annotation
 namespace: annotate
+scope: "public"
 description: Automated cell type annotation tool for scRNA-seq datasets on the basis of random forest.
 authors:
   - __merge__: /src/authors/jakub_majercik.yaml

src/annotate/random_forest_annotation/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: scanvi
 namespace: "annotate"
+scope: "public"
 description: |
   scANVI () is a semi-supervised model for single-cell transcriptomics data. scANVI is an scVI extension that can leverage the cell type knowledge for a subset of the cells present in the data sets to infer the states of the rest of the cells.
   This component will instantiate a scANVI model from a pre-trained scVI model, integrate the data and perform label prediction.

src/annotate/scanvi/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: svm_annotation
 namespace: annotate
+scope: "public"
 description: Automated cell type annotation tool for scRNA-seq datasets on the basis of SVMs.
 authors:
   - __merge__: /src/authors/jakub_majercik.yaml

src/annotate/svm_annotation/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: leiden
 namespace: "cluster"
+scope: "public"
 description: |
   Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. 
   Leiden is an improved version of the [Louvain algorithm] [Blondel08]. 

src/cluster/leiden/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: compress_h5mu
 namespace: "compression"
+scope: "public"
 description: |
   Compress a MuData file. 
 authors:

src/compression/compress_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: tar_extract
 namespace: compression
+scope: public
 status: deprecated
 description: Extract files from a tar archive
 arguments: