From f6667e1be25faabaa46024bafd6c9d4cc2408769 Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Mon, 19 Aug 2024 17:46:12 +0200 Subject: [PATCH 1/7] New version of Dockerfile --- dockerfiles/granie/Dockerfile | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/dockerfiles/granie/Dockerfile b/dockerfiles/granie/Dockerfile index 1cf5ed313..f3addab0d 100644 --- a/dockerfiles/granie/Dockerfile +++ b/dockerfiles/granie/Dockerfile @@ -7,13 +7,13 @@ FROM bioconductor/bioconductor_docker:devel-R-4.4.1 # libcurl4-openssl-dev \ # libxml2-dev \ # libssl-dev \ -# libcairo2-dev +# libcairo2-dev # libxt-dev \ # libopenblas-dev #Install R packages -RUN R -e "install.packages(c('devtools'))" +RUN R -e "install.packages(c('devtools', 'Signac'))" # Set the working directory WORKDIR /workspace @@ -21,19 +21,13 @@ WORKDIR /workspace # Default command CMD ["R"] -RUN R -e "remotes::install_version('Matrix', version = '1.6-3')" - #Version 1.9.4 of GRaNIE RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIE@855bf3def33ad7af9353db79c7e21c9279035fb8', host = 'git.embl.de', subdir = 'src/GRaNIE', dependencies = TRUE, upgrade = 'never')" #Version 0.2.1 of GRaNIEverse RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIEverse@3224b042f25f0085eeaf9194042bcb89103ea962', host = 'git.embl.de', upgrade = 'never', dependencies = TRUE)" -#There seems to be an incompatibility with the Matrix and irlba package, downgrading Matrix seems to work - -RUN R -e "install.packages('irlba',type='source')" +#There is an incompatibility with the Matrix and irlba package, see https://github.com/satijalab/seurat/issues/8000 +RUN R -e "install.packages('irlba',type='source', rebuild = TRUE)" RUN R -e "BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86', 'EnsDb.Mmusculus.v79', 'BSgenome.Mmusculus.UCSC.mm39'))" - - - From e79b7be5a2ba1096887acb9b700ef90f57f23048 Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Tue, 20 Aug 2024 01:22:59 +0200 Subject: [PATCH 2/7] viash config modifications + new image reference --- src/methods/multi_omics/granie/config.vsh.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index 55daf328d..affff1086 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -16,14 +16,14 @@ functionality: required: false direction: input description: "Path to the RNA data file (e.g., rna.rds)." - default: resources_test/grn-benchmark/multiomics_rna.rds + default: resources_test/grn-benchmark/multiomics_r/rna.rds - name: --file_atac type: file required: false direction: input description: "Path to the ATAC data file (e.g., atac.rds)." - default: resources_test/grn-benchmark/multiomics_atac.rds + default: resources_test/grn-benchmark/multiomics_r/atac.rds - name: --preprocessing_clusteringMethod @@ -117,7 +117,7 @@ functionality: platforms: - type: docker - image: chrarnold84/granieverse:latest + image: chrarnold84/granieverse:v1.1 - type: native - type: nextflow From 6540dd0917483f0ab8ca50bf0f75d50f57b86d38 Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Tue, 20 Aug 2024 23:25:52 +0200 Subject: [PATCH 3/7] granie updates --- dockerfiles/granie/Dockerfile | 23 +--- .../multi_omics/granie/config.vsh.yaml | 57 ++++++++- src/methods/multi_omics/granie/script.R | 120 +++++++++--------- 3 files changed, 123 insertions(+), 77 deletions(-) diff --git a/dockerfiles/granie/Dockerfile b/dockerfiles/granie/Dockerfile index f3addab0d..ee59a1b08 100644 --- a/dockerfiles/granie/Dockerfile +++ b/dockerfiles/granie/Dockerfile @@ -2,18 +2,8 @@ FROM bioconductor/bioconductor_docker:devel-R-4.4.1 -# Install required dependencies for the R packages -#RUN apt-get update && apt-get install -y \ -# libcurl4-openssl-dev \ -# libxml2-dev \ -# libssl-dev \ -# libcairo2-dev -# libxt-dev \ -# libopenblas-dev - - #Install R packages -RUN R -e "install.packages(c('devtools', 'Signac'))" +RUN R -e "install.packages(c('devtools'))" # Set the working directory WORKDIR /workspace @@ -21,13 +11,14 @@ WORKDIR /workspace # Default command CMD ["R"] -#Version 1.9.4 of GRaNIE -RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIE@855bf3def33ad7af9353db79c7e21c9279035fb8', host = 'git.embl.de', subdir = 'src/GRaNIE', dependencies = TRUE, upgrade = 'never')" +#Version 1.9.4 of GRaNIE. +RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIE@v1.9.4', host = 'git.embl.de', subdir = 'src/GRaNIE', dependencies = TRUE, upgrade = 'never')" -#Version 0.2.1 of GRaNIEverse -RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIEverse@3224b042f25f0085eeaf9194042bcb89103ea962', host = 'git.embl.de', upgrade = 'never', dependencies = TRUE)" +#Version 0.3.1 of GRaNIEverse +RUN R -e "devtools::install_gitlab('grp-zaugg/GRaNIEverse@v1.3.1', host = 'git.embl.de', upgrade = 'never', dependencies = TRUE)" #There is an incompatibility with the Matrix and irlba package, see https://github.com/satijalab/seurat/issues/8000 RUN R -e "install.packages('irlba',type='source', rebuild = TRUE)" -RUN R -e "BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86', 'EnsDb.Mmusculus.v79', 'BSgenome.Mmusculus.UCSC.mm39'))" +# biovizbase is only needed to create the ATAC assay along with annotation +RUN R -e "BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86', 'EnsDb.Mmusculus.v79', 'BSgenome.Mmusculus.UCSC.mm39', 'biovizBase', 'Signac', 'glmGamPoi'))" diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index affff1086..98997be5b 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -1,5 +1,5 @@ __merge__: ../../../api/comp_method.yaml - + functionality: name: granie @@ -25,6 +25,55 @@ functionality: description: "Path to the ATAC data file (e.g., atac.rds)." default: resources_test/grn-benchmark/multiomics_r/atac.rds + - name: --normRNA + type: string + required: false + direction: input + description: Normalization method for RNA data. + default: "SCT" + + - name: --normATAC + type: string + required: false + direction: input + description: Normalization method for ATAC data. + default: "LSI" + + - name: --LSI_featureCutoff + type: string + required: false + direction: input + description: Feature cutoff for LSI normalization. + default: "q0" + + - name: --nDimensions_ATAC + type: integer + required: false + direction: input + description: Number of dimensions for ATAC modality + default: 50 + + - name: --integrationMethod + type: string + required: false + direction: input + description: Method used for data integration. + default: "WNN" + + - name: --WNN_knn + type: integer + required: false + direction: input + description: Number of nearest neighbors for WNN integration. + default: 20 + + - name: --minCellsPerCluster + type: integer + required: false + direction: input + description: Minimum number of cells required per cluster. + default: 25 + - name: --preprocessing_clusteringMethod type: integer @@ -40,12 +89,12 @@ functionality: description: Resolution for clustering, typically between 5 and 20. default: 14 - - name: --preprocessing_SCT_nDimensions + - name: --preprocessing_RNA_nDimensions type: integer required: false direction: input default: 50 - description: Number of dimensions for SCT, default is 50. + description: Number of dimensions for RNA reduction, default is 50. - name: --genomeAssembly type: string @@ -117,7 +166,7 @@ functionality: platforms: - type: docker - image: chrarnold84/granieverse:v1.1 + image: chrarnold84/granieverse:v1.3 - type: native - type: nextflow diff --git a/src/methods/multi_omics/granie/script.R b/src/methods/multi_omics/granie/script.R index 3df0aeb83..a3aac6163 100644 --- a/src/methods/multi_omics/granie/script.R +++ b/src/methods/multi_omics/granie/script.R @@ -1,48 +1,55 @@ +## VIASH START +# par <- list( +# file_rna = "resources_test/grn-benchmark/multiomics_r/rna.rds", +# file_atac = "resources_test/grn-benchmark/multiomics_r/atac.rds", +# preprocessing_clusteringMethod = 1, # Seurat::FindClusters: (1 = original Louvain algorithm, 2 = Louvain algorithm with multilevel refinement, 3 = SLM algorithm, 4 = Leiden algorithm) +# preprocessing_clusterResolution = 14, # Typically between 5 and 20 +# preprocessing_RNA_nDimensions = 50, # Default 50 +# genomeAssembly = "hg38", +# GRaNIE_corMethod = "spearman", +# GRaNIE_includeSexChr = TRUE, +# GRaNIE_promoterRange = 250000, +# GRaNIE_TF_peak.fdr.threshold = 0.2, +# GRaNIE_peak_gene.fdr.threshold = 0.2, +# GRaNIE_nCores = 4, +# peak_gene = "output/granie/peak_gene.csv", # not yet implemented, should I? +# prediction= "output/granie/prediction.csv", +# useWeightingLinks = FALSE, +# forceRerun = FALSE +# ) + +# meta <- list( +# functionality_name = "my_method_r" +# ) +## VIASH END + set.seed(42) +suppressPackageStartupMessages(library(Seurat)) -library(Seurat) -library(Signac) -library(Matrix) +suppressPackageStartupMessages(library(Signac)) +suppressPackageStartupMessages(library(Matrix)) library(GRaNIEverse) library(GRaNIE) -library(qs) -library(BSgenome.Hsapiens.UCSC.hg38) -library(EnsDb.Hsapiens.v86) -library(EnsDb.Mmusculus.v79) -library(BSgenome.Mmusculus.UCSC.mm39) -library(dplyr) +suppressPackageStartupMessages(library(qs)) +suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg38)) +suppressPackageStartupMessages(library(EnsDb.Hsapiens.v86)) +suppressPackageStartupMessages(library(EnsDb.Mmusculus.v79)) +suppressPackageStartupMessages(library(BSgenome.Mmusculus.UCSC.mm39)) +suppressPackageStartupMessages(library(dplyr)) +suppressPackageStartupMessages(library(SummarizedExperiment)) + + +cat("Content of par list:") +str(par) + +#qs::qsave(par, "/home/carnold/par.qs") -## VIASH START -par <- list( - file_rna = "resources_test/grn-benchmark/multiomics_r/rna.rds", - file_atac = "resources_test/grn-benchmark/multiomics_r/atac.rds", - temp_dir = "output/granie/", - preprocessing_clusteringMethod = 1, # Seurat::FindClusters: (1 = original Louvain algorithm, 2 = Louvain algorithm with multilevel refinement, 3 = SLM algorithm, 4 = Leiden algorithm) - preprocessing_clusterResolution = 14, # Typically between 5 and 20 - preprocessing_SCT_nDimensions = 50, # Default 50 - genomeAssembly = "hg38", - GRaNIE_corMethod = "spearman", - GRaNIE_includeSexChr = TRUE, - GRaNIE_promoterRange = 250000, - GRaNIE_TF_peak_fdr_threshold = 0.2, - GRaNIE_peak_gene_fdr_threshold = 0.2, - num_workers = 4, - peak_gene = "output/granie/peak_gene.csv", # not yet implemented, should I? - prediction= "output/granie/prediction.csv", - useWeightingLinks = FALSE, - forceRerun = FALSE -) -## VIASH END -print(par) -# meta <- list( -# functionality_name = "my_method_r" -# ) #### STANDARD ASSIGNMENTS ### file_seurat = "seurat_granie.qs" -outputDir = par$temp_dir +outputDir = dirname(par$prediction) if (!dir.exists(outputDir)) { dir.create(outputDir, recursive = TRUE) @@ -91,7 +98,7 @@ if (!file.exists(file_RNA)) { # Preprocess data # ################### -if (par.l$forceRerun | !file.exists(file_seurat)) { +if (par$forceRerun | !file.exists(file_seurat)) { # Sparse matrix rna.m = readRDS(par$file_rna) @@ -146,12 +153,6 @@ if (par.l$forceRerun | !file.exists(file_seurat)) { } output_seuratProcessed = paste0(outputDir, "/seuratObject.qs") -if (!file.exists(output_seuratProcessed)) { - prepareData = TRUE -} else { - prepareData = FALSE -} - ################### # Preprocess data # @@ -162,24 +163,29 @@ GRaNIE_file_peaks = paste0(outputDir, "/atac.pseudobulkFromClusters_res", par$pr GRaNIE_file_rna = paste0(outputDir, "/rna.pseudobulkFromClusters_res", par$preprocessing_clusterResolution, "_mean.tsv.gz") GRaNIE_file_metadata = paste0(outputDir, "/metadata_res", par$preprocessing_clusterResolution, "_mean.tsv.gz") -if (file.exists(GRaNIE_file_peaks) & file.exists(GRaNIE_file_metadata) & file.exists(GRaNIE_file_rna) & !par.l$forceRerun) { +if (file.exists(GRaNIE_file_peaks) & file.exists(GRaNIE_file_metadata) & file.exists(GRaNIE_file_rna) & !par$forceRerun) { - cat("Preprocessing skipped because all files alreadx exist anf forceRerun = FALSE.") + cat("Preprocessing skipped because all files already exist anf forceRerun = FALSE.") } else { - + + #str(formals(prepareSeuratData_GRaNIE)) + seurat_object = prepareSeuratData_GRaNIE(seurat_object, - outputDir = par$outputDir, - file_RNA_features = file_RNA, - assayName_RNA_raw = "RNA", assayName_ATAC = "peaks", - prepareData = prepareData, - SCT_nDimensions = par$preprocessing_SCT_nDimensions, - dimensionsToIgnore_LSI_ATAC = 1, + outputDir = outputDir, + saveSeuratObject = TRUE, + genome = par$genomeAssembly, + assayName_RNA = "RNA", normRNA = "SCT", nDimensions_RNA = par$preprocessing_RNA_nDimensions, recalculateVariableFeatures = NULL, + assayName_ATAC_raw = "peaks", + normATAC = "LSI", LSI_featureCutoff = "q0", nDimensions_ATAC = 50, dimensionsToIgnore_LSI_ATAC = 1, + integrationMethod = "WNN", WNN_knn = 20, pseudobulk_source = "cluster", countAggregation = "mean", clusteringAlgorithm = par$preprocessing_clusteringMethod, - clusterResolutions = par$preprocessing_clusterResolution, - saveSeuratObject = TRUE) + clusterResolutions = par$preprocessing_clusterResolution, + minCellsPerCluster = 25, + forceRerun = FALSE + ) } @@ -190,7 +196,7 @@ if (file.exists(GRaNIE_file_peaks) & file.exists(GRaNIE_file_metadata) & file.ex ############## GRN = runGRaNIE( - dir_output = par$temp_dir, + dir_output = outputDir, datasetName = "undescribed", GRaNIE_file_peaks, GRaNIE_file_rna, @@ -210,11 +216,11 @@ GRN = runGRaNIE( corMethod = par$GRaNIE_corMethod, promoterRange = par$GRaNIE_promoterRange, useGCCorrection = FALSE, - TF_peak.fdr.threshold = par$GRaNIE_TF_peak_fdr_threshold, - peak_gene.fdr.threshold = par$GRaNIE_peak_gene_fdr_threshold, + TF_peak.fdr.threshold = par$GRaNIE_TF_peak.fdr.threshold, + peak_gene.fdr.threshold = par$GRaNIE_peak_gene.fdr.threshold, runTFClassification = FALSE, runNetworkAnalyses = FALSE, - nCores = par$num_workers, + nCores = par$GRaNIE_nCores, forceRerun = TRUE ) From c61117d724c19d3130c745b758ff99fd8800dd4b Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Wed, 21 Aug 2024 13:19:52 +0200 Subject: [PATCH 4/7] fixes --- src/methods/multi_omics/granie/config.vsh.yaml | 9 ++++++++- src/methods/multi_omics/granie/script.R | 13 +++++++++++-- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index 98997be5b..07527f80c 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -1,5 +1,5 @@ __merge__: ../../../api/comp_method.yaml - + functionality: name: granie @@ -159,6 +159,13 @@ functionality: direction: input description: "Flag to force rerun of the analysis regardless of existing results." + - name: --subset + type: boolean + required: false + default: True + direction: input + description: "Flag for testing purposes to subset the data for faster running times" + resources: - type: r_script path: script.R diff --git a/src/methods/multi_omics/granie/script.R b/src/methods/multi_omics/granie/script.R index a3aac6163..695ec3e16 100644 --- a/src/methods/multi_omics/granie/script.R +++ b/src/methods/multi_omics/granie/script.R @@ -74,7 +74,7 @@ if (!file.exists(destfile)) { # Define the directory to extract the files to exdir <- "PWMScan_HOCOMOCOv12_H12INVIVO" -GRaNIE_TFBSFolder = paste0(exdir, "/PWMScan_HOCOMOCOv12/H12INVIVO") +GRaNIE_TFBSFolder = paste0(exdir, "/H12INVIVO") if (!file.exists(GRaNIE_TFBSFolder)) { untar(destfile, exdir = exdir) @@ -169,7 +169,16 @@ if (file.exists(GRaNIE_file_peaks) & file.exists(GRaNIE_file_metadata) & file.ex } else { - #str(formals(prepareSeuratData_GRaNIE)) + # Subset for testing purposes + if (par$subset == TRUE) { + cat("SUBSET cells\n") + random_cells <- sample(Cells(seurat_object), size = 5000, replace = FALSE) + seurat_object = subset(seurat_object, cells = random_cells) + cat("SUBSET peaks\n") + peak_names <- rownames(seurat_object[["peaks"]]) + selected_peaks <- sample(peak_names, size = 50000, replace = FALSE) + seurat_object[["peaks"]] = subset(seurat_object[["peaks"]], features = selected_peaks) + } seurat_object = prepareSeuratData_GRaNIE(seurat_object, outputDir = outputDir, From 54d1676476c71c857e07b8fee995d7d620fa5078 Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Wed, 21 Aug 2024 14:48:20 +0200 Subject: [PATCH 5/7] fixes --- src/methods/multi_omics/granie/config.vsh.yaml | 15 ++++++++------- src/methods/multi_omics/granie/script.R | 12 ++++++------ 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index 07527f80c..0cf1612ae 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -123,7 +123,7 @@ functionality: default: 250000 direction: input description: Range in base pairs for maximum distance of peak-gene connections (default is 250000). - +--GRaNIE_includeSexChr - name: --GRaNIE_TF_peak_fdr_threshold type: double required: false @@ -138,12 +138,13 @@ functionality: direction: input description: FDR threshold for peak-gene connections (default is 0.2). - - name: --peak_gene - type: file - required: false - direction: output - description: Path to the peak-gene output file (e.g., peak_gene.csv). Not yet implemented. - default: output/granie/peak_gene.csv + # File existance is checked, so commenting out for now + # - name: --peak_gene + # type: file + # required: false + # direction: output + # description: Path to the peak-gene output file (e.g., peak_gene.csv). Not yet implemented. + # default: output/granie/peak_gene.csv - name: --useWeightingLinks type: boolean diff --git a/src/methods/multi_omics/granie/script.R b/src/methods/multi_omics/granie/script.R index 695ec3e16..c8709be90 100644 --- a/src/methods/multi_omics/granie/script.R +++ b/src/methods/multi_omics/granie/script.R @@ -10,9 +10,9 @@ # GRaNIE_corMethod = "spearman", # GRaNIE_includeSexChr = TRUE, # GRaNIE_promoterRange = 250000, -# GRaNIE_TF_peak.fdr.threshold = 0.2, -# GRaNIE_peak_gene.fdr.threshold = 0.2, -# GRaNIE_nCores = 4, +# GRaNIE_TF_peak_fdr_threshold = 0.2, +# GGRaNIE_peak_gene_fdr_threshold = 0.2, +# num_workers = 4, # peak_gene = "output/granie/peak_gene.csv", # not yet implemented, should I? # prediction= "output/granie/prediction.csv", # useWeightingLinks = FALSE, @@ -225,11 +225,11 @@ GRN = runGRaNIE( corMethod = par$GRaNIE_corMethod, promoterRange = par$GRaNIE_promoterRange, useGCCorrection = FALSE, - TF_peak.fdr.threshold = par$GRaNIE_TF_peak.fdr.threshold, - peak_gene.fdr.threshold = par$GRaNIE_peak_gene.fdr.threshold, + TF_peak.fdr.threshold = par$GRaNIE_TF_peak_fdr_threshold, + peak_gene.fdr.threshold = par$GRaNIE_peak_gene_fdr_threshold, runTFClassification = FALSE, runNetworkAnalyses = FALSE, - nCores = par$GRaNIE_nCores, + nCores = par$num_workers, forceRerun = TRUE ) From b52a52b07d8c1f80028ae6d8f8bd49557146876c Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Wed, 21 Aug 2024 14:51:06 +0200 Subject: [PATCH 6/7] fixes --- src/methods/multi_omics/granie/config.vsh.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index 0cf1612ae..e32288090 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -123,7 +123,7 @@ functionality: default: 250000 direction: input description: Range in base pairs for maximum distance of peak-gene connections (default is 250000). ---GRaNIE_includeSexChr + - name: --GRaNIE_TF_peak_fdr_threshold type: double required: false @@ -138,7 +138,7 @@ functionality: direction: input description: FDR threshold for peak-gene connections (default is 0.2). - # File existance is checked, so commenting out for now + # Existance of output files is checked, not yet implemented # - name: --peak_gene # type: file # required: false @@ -163,7 +163,7 @@ functionality: - name: --subset type: boolean required: false - default: True + default: true direction: input description: "Flag for testing purposes to subset the data for faster running times" From ce58d0967928946c375350f5af5b99c2ff2d81a2 Mon Sep 17 00:00:00 2001 From: Christian Arnold Date: Wed, 21 Aug 2024 15:27:01 +0200 Subject: [PATCH 7/7] Change subset back to false --- src/methods/multi_omics/granie/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/methods/multi_omics/granie/config.vsh.yaml b/src/methods/multi_omics/granie/config.vsh.yaml index e32288090..151c545cc 100644 --- a/src/methods/multi_omics/granie/config.vsh.yaml +++ b/src/methods/multi_omics/granie/config.vsh.yaml @@ -163,7 +163,7 @@ functionality: - name: --subset type: boolean required: false - default: true + default: false direction: input description: "Flag for testing purposes to subset the data for faster running times"