update format

_viash.yaml

@@ -76,6 +76,12 @@ repositories:
     type: github
     repo: openproblems-bio/openproblems-v2
     tag: main_build
+  - name: core
+    type: github
+    repo: openproblems-bio/core
+    # tag: build/main
+    tag: build/add_common_components
+    path: viash/core
 
 config_mods: |
   .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }

src/methods/scdesign2/config.vsh.yaml

@@ -7,12 +7,11 @@ description: |
   scDesign2 is a transparent simulator that achieves all three goals (preserving genes, capturing gene correlations, and generating any 
   number of cells with varying sequencing depths) and generates high-fidelity synthetic data for multiple single-cell gene expression 
   count-based technologies.
-
 references:
   doi: 10.1186/s13059-021-02367-2
-info:
-  documentation_url: https://htmlpreview.github.io/?https://github.com/JSB-UCLA/scDesign2/blob/master/vignettes/scDesign2.html
-  repository_url: https://github.com/JSB-UCLA/scDesign2
+links:
+  documentation: https://htmlpreview.github.io/?https://github.com/JSB-UCLA/scDesign2/blob/master/vignettes/scDesign2.html
+  repository: https://github.com/JSB-UCLA/scDesign2
 
 resources:
   - type: r_script

src/methods/scdesign3/config.vsh.yaml

@@ -11,10 +11,9 @@ description: |
   trajectories and spatial locations).
 references:
   doi: 10.1038/s41587-023-01772-1
-
-info:
-  documentation_url: https://www.bioconductor.org/packages/release/bioc/html/scDesign3.html
-  repository_url: https://github.com/SONGDONGYUAN1994/scDesign3
+links:
+  documentation: https://www.bioconductor.org/packages/release/bioc/html/scDesign3.html
+  repository: https://github.com/SONGDONGYUAN1994/scDesign3
 
 arguments:
   - name: "--family"

src/methods/sparsim/config.vsh.yaml

@@ -8,10 +8,9 @@ description: |
   It allows to generate count data that resemble real data in terms of count intensity, variability and sparsity.
 references:
   doi: 10.1093/bioinformatics/btz752
-
-info:
-  documentation_url: https://gitlab.com/sysbiobig/sparsim/-/blob/master/vignettes/sparsim.Rmd
-  repository_url: https://gitlab.com/sysbiobig/sparsim
+links:
+  documentation: https://gitlab.com/sysbiobig/sparsim/-/blob/master/vignettes/sparsim.Rmd
+  repository: https://gitlab.com/sysbiobig/sparsim
 
 resources:
   - type: r_script
@@ -24,7 +23,7 @@ engines:
       - type: apt
         packages: [git, r-bioc-singlecellexperiment]
       - type: r
-        gitlab: sysbiobig/sparsim
+        gitlab: sysbiobig/SPARSim
 
 runners:
   - type: executable

src/methods/splatter/config.vsh.yaml

@@ -7,10 +7,9 @@ description: |
   The Splat model is a gamma-Poisson distribution used to generate a gene by cell matrix of counts. Mean expression levels for each gene are simulated from a gamma distribution and the Biological Coefficient of Variation is used to enforce a mean-variance trend before counts are simulated from a Poisson distribution.
 references:
   doi: 10.1186/s13059-017-1305-0
-
-info:
-  documentation_url: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
-  repository_url: https://github.com/Oshlack/splatter
+links:
+  documentation: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
+  repository: https://github.com/Oshlack/splatter
 
 resources:
   - type: r_script

src/methods/srtsim/config.vsh.yaml

@@ -8,10 +8,9 @@ description: |
   preserve spatial expression patterns, enabling evaluation of SRT method performance using synthetic data. 
 references:
   doi: 10.1186/s13059-023-02879-z
-
-info:
-  documentation_url: https://xzhoulab.github.io/SRTsim
-  repository_url: https://github.com/xzhoulab/srtsim
+links:
+  documentation: https://xzhoulab.github.io/SRTsim
+  repository: https://github.com/xzhoulab/srtsim
 
 resources:
   - type: r_script

src/methods/symsim/config.vsh.yaml

@@ -8,10 +8,9 @@ description: |
   and technical variation from measurement noise and bias.
 references:
   doi: 10.1038/s41467-019-10500-w
-
-info:
-  documentation_url: https://github.com/YosefLab/SymSim/blob/master/vignettes/SymSimTutorial.Rmd
-  repository_url: https://github.com/YosefLab/SymSim
+links:
+  documentation: https://github.com/YosefLab/SymSim/blob/master/vignettes/SymSimTutorial.Rmd
+  repository: https://github.com/YosefLab/SymSim
 
 resources:
   - type: r_script

src/methods/zinbwave/config.vsh.yaml

@@ -8,10 +8,9 @@ description: |
   of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data.
 references:
   doi: 10.1038/s41467-017-02554-5
-
-info:
-  documentation_url: https://bioconductor.org/packages/release/bioc/html/zinbwave.html
-  repository_url: https://github.com/drisso/zinbwave
+links:
+  documentation: https://bioconductor.org/packages/release/bioc/html/zinbwave.html
+  repository: https://github.com/drisso/zinbwave
 
 resources:
   - type: r_script

src/metrics/downstream/config.vsh.yaml

@@ -11,8 +11,9 @@ info:
         Adjusted Rand Index used in spatial clustering to measure the similarity between two data clusterings, adjusted for chance.
       references: 
         doi: 10.1145/1553374.1553511
-      documentation_url: https://cran.r-project.org/web/packages/aricode/index.html
-      repository_url: https://github.com/jchiquet/aricode
+      links:
+        documentation: https://cran.r-project.org/web/packages/aricode/index.html
+        repository: https://github.com/jchiquet/aricode
       min: -Inf
       max: +Inf
       maximize: true
@@ -23,8 +24,9 @@ info:
         Normalized Mutual Information used in spatial clustering to measure the agreement between two different clusterings, scaled to [0, 1].
       references:
         doi: 10.1145/1553374.1553511
-      documentation_url: https://cran.r-project.org/web/packages/aricode/index.html
-      repository_url: https://github.com/jchiquet/aricode
+      links:
+        documentation: https://cran.r-project.org/web/packages/aricode/index.html
+        repository: https://github.com/jchiquet/aricode
       min: 0
       max: 1
       maximize: true
@@ -55,8 +57,9 @@ info:
         Root Mean Squared Error used in cell type deconvolution to measure the difference between observed and predicted values.
       references: 
         doi: 10.5194/gmd-15-5481-2022
-      documentation_url: https://cran.r-project.org/web/packages/Metrics/Metrics.pdf
-      repository_url: https://github.com/mfrasco/Metrics
+      links:
+        documentation: https://cran.r-project.org/web/packages/Metrics/Metrics.pdf
+        repository: https://github.com/mfrasco/Metrics
       min: 0
       max: +Inf
       maximize: false
@@ -67,8 +70,9 @@ info:
         Jensen-Shannon Divergence used in cell type deconvolution to measure the similarity between two probability distributions.
       references: 
         doi: 10.21105/joss.00765
-      documentation_url: https://cran.r-project.org/web/packages/philentropy/index.html
-      repository_url: https://github.com/drostlab/philentropy
+      links:
+        documentation: https://cran.r-project.org/web/packages/philentropy/index.html
+        repository: https://github.com/drostlab/philentropy
       min: 0
       max: 1
       maximize: false
@@ -79,8 +83,9 @@ info:
         Mantel statistic used in spatial cross-correlation to test the correlation between two distance matrices.
       references: 
         doi: 10.1111/2041-210X.12425
-      documentation_url: https://search.r-project.org/CRAN/refmans/vegan/html/mantel.html
-      repository_url: https://github.com/vegandevs/vegan
+      links:
+        documentation: https://search.r-project.org/CRAN/refmans/vegan/html/mantel.html
+        repository: https://github.com/vegandevs/vegan
       min: -1
       max: 1
       maximize: true
@@ -91,8 +96,9 @@ info:
         Cosine similarity used in spatial cross-correlation to measure the cosine of the angle between two non-zero vectors.
       references: 
         doi: 10.1002/asi.20130
-      documentation_url: https://cran.r-project.org/web/packages/lsa/lsa.pdf
-      repository_url: https://github.com/cran/lsa
+      links:
+        documentation: https://cran.r-project.org/web/packages/lsa/lsa.pdf
+        repository: https://github.com/cran/lsa
       min: 0
       max: 1
       maximize: true

src/metrics/ks_statistic_gene_cell/config.vsh.yaml

@@ -3,10 +3,11 @@ __merge__: ../../api/comp_metric.yaml
 name: ks_statistic_gene_cell
 
 
-info:
-  documentation_url: https://cran.r-project.org/web/packages/ks/ks.pdf
-  repository_url: https://cran.r-project.org/web/packages/ks
+links:
+  documentation: https://cran.r-project.org/web/packages/ks/ks.pdf
+  repository: https://cran.r-project.org/web/packages/ks
 
+info:
   metrics:
     - name: ks_statistic_frac_zero_genes
       label: Fraction of zeros per gene

src/metrics/ks_statistic_sc_features/config.vsh.yaml

@@ -2,9 +2,11 @@ __merge__: ../../api/comp_metric.yaml
 
 name: ks_statistic_sc_features
 
+links:
+  documentation: https://cran.r-project.org/web/packages/ks/ks.pdf
+  repository: https://cran.r-project.org/web/packages/ks/
+
 info:
-  documentation_url: https://cran.r-project.org/web/packages/ks/ks.pdf
-  repository_url: https://cran.r-project.org/web/packages/ks/
   metrics:
     - name: ks_statistic_L_stats
       label: L statistics

src/metrics/ks_statistic_spatial/config.vsh.yaml

@@ -2,10 +2,11 @@ __merge__: ../../api/comp_metric.yaml
 
 name: ks_statistic_spatial
 
-info:
-  documentation_url: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ks_2samp.html
-  repository_url: https://github.com/scipy/scipy/
+links:
+  documentation: https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ks_2samp.html
+  repository: https://github.com/scipy/scipy/
 
+info:
   metrics:
     - name: ks_statistic_transition_matrix
       label: Transition matrix

src/workflows/run_benchmark/config.vsh.yaml

@@ -57,6 +57,8 @@ dependencies:
   - name: methods/srtsim
   - name: methods/symsim
   - name: methods/zinbwave
+  - name: control_methods/positive
+  - name: control_methods/negative
   - name: metrics/ks_statistic_gene_cell
   - name: metrics/ks_statistic_sc_features
   - name: metrics/ks_statistic_spatial

src/workflows/run_benchmark/main.nf

@@ -13,7 +13,9 @@ methods = [
   splatter,
   srtsim,
   symsim,
-  zinbwave
+  zinbwave,
+  positive,
+  negative
 ]
 
 // construct list of metrics