Add scope to configs

CHANGELOG.md

@@ -26,6 +26,8 @@
 
 * Add missing descriptions to components and arguments (PR #1018).
 
+* Add `scope` to component and workflow configurations (see https://viash.io/reference/config/scope.html) (PR #1013).
+
 ## BUG FIXES
 
 * Bump viash to 0.9.4. This adds support for nextflow versions starting major version 25.01 and fixes an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #1016).

src/annotate/celltypist/config.vsh.yaml

@@ -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/onclass/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/popv/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/random_forest_annotation/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/scanvi/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/svm_annotation/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/cluster/leiden/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/compression/compress_h5mu/config.vsh.yaml

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

src/compression/tar_extract/config.vsh.yaml

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

src/convert/from_10xh5_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_10xh5_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Converts a 10x h5 into an h5mu file.
 authors:

src/convert/from_10xmtx_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_10xmtx_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Converts a 10x mtx into an h5mu file.
 authors:

src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_bd_to_10x_molecular_barcode_tags"
 namespace: "convert"
+scope: "public"
 description: |
   Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB).
 authors:

src/convert/from_bdrhap_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_bdrhap_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.
 authors:

src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_cellranger_multi_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Converts the output from cellranger multi to a single .h5mu file.
   By default, will map the following library type names to modality names:

src/convert/from_h5ad_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: from_h5ad_to_h5mu
 namespace: "convert"
+scope: "public"
 description: |
   Converts a single layer h5ad file into a single MuData object
 authors:

src/convert/from_h5ad_to_seurat/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_h5ad_to_seurat"
 namespace: "convert"
+scope: "public"
 description: |
   Converts an h5ad file into a Seurat file.
 authors:

src/convert/from_h5mu_to_h5ad/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: from_h5mu_to_h5ad
 namespace: "convert"
+scope: "public"
 description: |
   Converts a h5mu file into a h5ad file.
 authors:

src/convert/from_h5mu_to_seurat/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_h5mu_to_seurat"
 namespace: "convert"
+scope: "public"
 description: |
   Converts an h5mu file into a Seurat file.
 

src/correction/cellbender_remove_background/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: cellbender_remove_background
 namespace: "correction"
+scope: "public"
 description: |
   Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.
 

src/correction/cellbender_remove_background_v0_2/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: cellbender_remove_background_v0_2
 namespace: "correction"
+scope: "public"
 description: |
   Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.
 

src/dataflow/concatenate_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: concatenate_h5mu
 namespace: "dataflow"
+scope: "public"
 description: |
   Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.
 authors:

src/dataflow/merge/config.vsh.yml

@@ -1,5 +1,6 @@
 name: merge
 namespace: "dataflow"
+scope: "public"
 description: |
   Combine one or more single-modality .h5mu files together into one .h5mu file.
 authors:

src/dataflow/split_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: split_h5mu
 namespace: "dataflow"
+scope: "public"
 description: |
   Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. 
 authors:

src/dataflow/split_modalities/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: split_modalities
 namespace: "dataflow"
+scope: "public"
 description: |
   Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. 
 authors:

src/demux/bcl2fastq/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: bcl2fastq
 namespace: demux
+scope: "public"
 description: |
   Convert bcl files to fastq files using bcl2fastq.
 authors:

src/demux/bcl_convert/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: bcl_convert
 namespace: demux
+scope: "public"
 description: |
   Convert bcl files to fastq files using bcl-convert.
   Information about upgrading from bcl2fastq via

src/demux/cellranger_atac_mkfastq/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: cellranger_atac_mkfastq
 namespace: demux
+scope: "public"
 description: Demultiplex raw sequencing data for ATAC experiments
 usage: |
   cellranger_atac_mkfastq \

src/demux/cellranger_mkfastq/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: cellranger_mkfastq
 namespace: demux
+scope: "public"
 description: Demultiplex raw sequencing data
 usage: |
   cellranger_mkfastq \

src/dimred/densmap/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: densmap
 namespace: "dimred"
+scope: "public"
 description: |
   A modification of UMAP that adds an extra cost term in order to preserve information 
   about the relative local density of the data. It is performed on the same inputs as UMAP.

src/dimred/lsi/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: lsi
 namespace: "dimred"
+scope: "public"
 description: |
   Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.
 authors:

src/dimred/pca/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: pca
 namespace: "dimred"
+scope: "public"
 description: |
   Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].
 authors:

src/dimred/tsne/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: tsne
 namespace: "dimred"
+scope: "public"
 description: |
   t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality reduction technique used to visualize high-dimensional data in a low-dimensional space, revealing patterns and clusters by preserving local data similarities.
 authors:

src/dimred/umap/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: umap
 namespace: "dimred"
+scope: "public"
 description: |
   UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint.
 authors:

src/download/download_file/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "download_file"
 namespace: "download"
+scope: "test"
 status: "deprecated"
 description: |
   Download a file.

src/download/sync_test_resources/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "sync_test_resources"
 namespace: "download"
+scope: "test"
 description: Sync test resources to the local filesystem
 usage: |
   sync_test_resources

src/feature_annotation/align_query_reference/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: align_query_reference
 namespace: feature_annotation
+scope: "public"
 description: |
   Alignment of a query and reference dataset by:
   * Alignment of layers

src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: highly_variable_features_scanpy
 namespace: feature_annotation
+scope: "public"
 description: |
   Annotate highly variable features [Satija15] [Zheng17] [Stuart19].
 

src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: score_genes_cell_cycle_scanpy
 namespace: feature_annotation
+scope: "public"
 authors:
   - __merge__: /src/authors/robrecht_cannoodt.yaml
     roles: [ author ]

src/feature_annotation/score_genes_scanpy/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: score_genes_scanpy
 namespace: feature_annotation
+scope: "public"
 authors:
   - __merge__: /src/authors/robrecht_cannoodt.yaml
     roles: [ author ]

src/files/make_params/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: make_params
 namespace: "files"
+scope: "public"
 description: "Looks for files in a directory and turn it in a params file."
 authors:
   - __merge__: /src/authors/angela_pisco.yaml

src/filter/delimit_fraction/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: delimit_fraction
 namespace: "filter"
+scope: "public"
 description: |
   Turns a column containing values between 0 and 1 into a boolean column based on thresholds.
 authors:

src/filter/do_filter/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: do_filter
 namespace: "filter"
+scope: "public"
 description: |
   Remove observations and variables based on specified .obs and .var columns.
 authors:

src/filter/filter_with_counts/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: filter_with_counts
 namespace: "filter"
+scope: "public"
 description: |
   Filter scRNA-seq data based on the primary QC metrics. 
   This is based on both the UMI counts, the gene counts 

src/filter/filter_with_scrublet/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: filter_with_scrublet
 namespace: "filter"
+scope: "public"
 description: |
   Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).
   The method tests for potential doublets by using the expression profiles of

src/filter/intersect_obs/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: intersect_obs
 namespace: "filter"
+scope: "public"
 description: |
   Create an intersection between two or more modalities.
 

src/filter/remove_modality/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: remove_modality
 namespace: "filter"
+scope: "public"
 description: |
   Remove a modality from a .h5mu file
 authors:

src/filter/subset_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: subset_h5mu
 namespace: "filter"
+scope: "public"
 description: |
   Create a subset of a mudata file by selecting the first number of observations
 authors:

src/filter/subset_obsp/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: subset_obsp
 namespace: "filter"
+scope: "public"
 description: |
   Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot.
 authors:

src/genetic_demux/bcftools/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: bcftools
 namespace: genetic_demux
+scope: "public"
 description: Filter the variants called by freebayes or cellSNP
 authors:
   - __merge__: /src/authors/xichen_wu.yaml

src/genetic_demux/cellsnp/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: cellsnp
 namespace: genetic_demux
+scope: "public"
 description: "cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data. It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo."
 authors:
   - __merge__: /src/authors/xichen_wu.yaml

src/genetic_demux/demuxlet/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: demuxlet
 namespace: genetic_demux
+scope: "public"
 description: |
   Demuxlet is a software tool to deconvolute sample identity and identify multiplets when
   multiple samples are pooled by barcoded single cell sequencing. If external genotyping data

src/genetic_demux/dsc_pileup/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: dsc_pileup
 namespace: genetic_demux
+scope: "public"
 description: |
   Dsc-pileup is a software tool to pileup reads and corresponding base quality 
   for each overlapping SNPs and each barcode. By using pileup files,

src/genetic_demux/freebayes/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: freebayes
 namespace: genetic_demux
+scope: "public"
 description: |
   Freebayes is a Bayesian genetic variant detector designed to
   find small polymorphisms, specifically SNPs.

src/genetic_demux/freemuxlet/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: freemuxlet
 namespace: genetic_demux
+scope: "public"
 description: |
   Freemuxlet is a software tool to deconvolute sample identity and identify multiplets when
   multiple samples are pooled by barcoded single cell sequencing. If external genotyping

src/genetic_demux/samtools/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: samtools
 namespace: genetic_demux
+scope: "public"
 description: Filter the BAM according to the instruction of scSplit via Samtools.
 authors:
   - __merge__: /src/authors/xichen_wu.yaml