diff --git a/_viash.yaml b/_viash.yaml index 77433cb8..f23b139e 100644 --- a/_viash.yaml +++ b/_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" } diff --git a/common b/common index a1409176..1660eef0 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit a1409176da317c8a7c9c65d1488bcf3b5afee3d6 +Subproject commit 1660eef0b1172c1059270fff77f9abc0a5fc1ea4 diff --git a/src/methods/scdesign2/config.vsh.yaml b/src/methods/scdesign2/config.vsh.yaml index 12939750..ac7a562a 100644 --- a/src/methods/scdesign2/config.vsh.yaml +++ b/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 diff --git a/src/methods/scdesign3/config.vsh.yaml b/src/methods/scdesign3/config.vsh.yaml index 7b3814f1..5d8b7c5a 100644 --- a/src/methods/scdesign3/config.vsh.yaml +++ b/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" diff --git a/src/methods/sparsim/config.vsh.yaml b/src/methods/sparsim/config.vsh.yaml index 79e77c8f..d0331252 100644 --- a/src/methods/sparsim/config.vsh.yaml +++ b/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 diff --git a/src/methods/splatter/config.vsh.yaml b/src/methods/splatter/config.vsh.yaml index f798daf5..aaf6c6a3 100644 --- a/src/methods/splatter/config.vsh.yaml +++ b/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 diff --git a/src/methods/srtsim/config.vsh.yaml b/src/methods/srtsim/config.vsh.yaml index c21270fe..da146a17 100644 --- a/src/methods/srtsim/config.vsh.yaml +++ b/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 diff --git a/src/methods/symsim/config.vsh.yaml b/src/methods/symsim/config.vsh.yaml index 63031199..bb389120 100644 --- a/src/methods/symsim/config.vsh.yaml +++ b/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 diff --git a/src/methods/zinbwave/config.vsh.yaml b/src/methods/zinbwave/config.vsh.yaml index aec8c26a..1b882d01 100644 --- a/src/methods/zinbwave/config.vsh.yaml +++ b/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 diff --git a/src/metrics/downstream/config.vsh.yaml b/src/metrics/downstream/config.vsh.yaml index 7fcdc1cd..fcd164a6 100644 --- a/src/metrics/downstream/config.vsh.yaml +++ b/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 diff --git a/src/metrics/ks_statistic_gene_cell/config.vsh.yaml b/src/metrics/ks_statistic_gene_cell/config.vsh.yaml index 34a8e95b..59ceb977 100644 --- a/src/metrics/ks_statistic_gene_cell/config.vsh.yaml +++ b/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 diff --git a/src/metrics/ks_statistic_sc_features/config.vsh.yaml b/src/metrics/ks_statistic_sc_features/config.vsh.yaml index 1cd76510..7e22f428 100644 --- a/src/metrics/ks_statistic_sc_features/config.vsh.yaml +++ b/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 diff --git a/src/metrics/ks_statistic_spatial/config.vsh.yaml b/src/metrics/ks_statistic_spatial/config.vsh.yaml index 7aa21173..34d90d34 100644 --- a/src/metrics/ks_statistic_spatial/config.vsh.yaml +++ b/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 diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml index 8e0dab3e..efaa3f04 100644 --- a/src/workflows/run_benchmark/config.vsh.yaml +++ b/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 diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf index 2c182503..322f8277 100644 --- a/src/workflows/run_benchmark/main.nf +++ b/src/workflows/run_benchmark/main.nf @@ -13,7 +13,9 @@ methods = [ splatter, srtsim, symsim, - zinbwave + zinbwave, + positive, + negative ] // construct list of metrics