granie failed to load seuratobject

openproblems-bio · Aug 16, 2024 · 238e004 · 238e004
1 parent 140fc46
commit 238e004
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diff --git a/...hods/multi_omics/granie/config.novsh.yaml → ...ethods/multi_omics/granie/config.vsh.yaml b/...hods/multi_omics/granie/config.novsh.yaml → ...ethods/multi_omics/granie/config.vsh.yaml
@@ -2,33 +2,29 @@ __merge__: ../../../api/comp_method.yaml
 
 
 functionality:
-  name: GRaNIE
+  name: granie
   namespace: "grn_methods"
   info:
-    label: GRaNIE
+    label: granie
     summary: "GRN inference using GRaNIE"
     description: |
       GRN inference using GRaNIE
     documentation_url: https://grp-zaugg.embl-community.io/GRaNIE/
   arguments:
   - name: --file_rna
     type: file
-    required: true
+    required: false
     direction: input
     description: "Path to the RNA data file (e.g., rna.rds)."
+    default: resources_test/grn-benchmark/multiomics_rna.rds
 
   - name: --file_atac
     type: file
-    required: true
+    required: false
     direction: input
     description: "Path to the ATAC data file (e.g., atac.rds)."
+    default: resources_test/grn-benchmark/multiomics_atac.rds
 
-  - name: --temp_dir
-    type: directory
-    required: false
-    direction: input
-    default: "output/granie/"
-    description: "Temporary directory for output files."
 
   - name: --preprocessing_clusteringMethod
     type: integer
@@ -38,76 +34,67 @@ functionality:
     description: "Seurat::FindClusters: Clustering method to use (1 = original Louvain algorithm, 2 = Louvain algorithm with multilevel refinement, 3 = SLM algorithm, 4 = Leiden algorithm)."
 
   - name: --preprocessing_clusterResolution
-    type: float
-    required: true
+    type: double
+    required: false
     direction: input
-    description: "Resolution for clustering, typically between 5 and 20."
+    description: Resolution for clustering, typically between 5 and 20.
+    default: 14
 
   - name: --preprocessing_SCT_nDimensions
     type: integer
     required: false
     direction: input
     default: 50
-    description: "Number of dimensions for SCT, default is 50."
+    description: Number of dimensions for SCT, default is 50.
 
   - name: --genomeAssembly
     type: string
-    required: true
+    required: false
     direction: input
-    description: "Genome assembly version (e.g., hg38). Currently, hg38 and mm10 is supported."
+    description: Genome assembly version (e.g., hg38). Currently, hg38 and mm10 is supported.
+    default: hg38
 
   - name: --GRaNIE_corMethod
     type: string
     required: false
-    default: "spearman"
+    default: spearman
     direction: input
-    description: "Correlation method used in GRaNIE (e.g., 'spearman')."
+    description: Correlation method used in GRaNIE (e.g., 'spearman').
 
   - name: --GRaNIE_includeSexChr
     type: boolean
     required: false
     default: true
     direction: input
-    description: "Include sex chromosomes in analysis."
+    description: Include sex chromosomes in analysis.
 
   - name: --GRaNIE_promoterRange
     type: integer
     required: false
     default: 250000
     direction: input
-    description: "Range in base pairs for maximum distance of peak-gene connections (default is 250000)."
+    description: Range in base pairs for maximum distance of peak-gene connections (default is 250000).
 
-  - name: --GRaNIE_TF_peak.fdr.threshold
-    type: float
+  - name: --GRaNIE_TF_peak_fdr_threshold
+    type: double
     required: false
     default: 0.2
     direction: input
-    description: "FDR threshold for TF-peak connections (default is 0.2)."
+    description: FDR threshold for TF-peak connections (default is 0.2).
 
-  - name: --GRaNIE_peak_gene.fdr.threshold
-    type: float
+  - name: --GRaNIE_peak_gene_fdr_threshold
+    type: double
     required: false
     default: 0.2
     direction: input
-    description: "FDR threshold for peak-gene connections (default is 0.2)."
-
-  - name: --GRaNIE_nCores
-    type: integer
-    required: true
-    direction: input
-    description: "Number of cores to use for computation (default is 4)."
+    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."
-
-  - name: --prediction
-    type: file
-    required: true
-    direction: output
-    description: "Path to the prediction output file (e.g., prediction.csv)."
+    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
@@ -14,31 +14,31 @@ library(BSgenome.Mmusculus.UCSC.mm39)
 library(dplyr)
 
 ## 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,
-#   GRaNIE_nCores = 4,
-#   peak_gene = "output/granie/peak_gene.csv", # not yet implemented, should I?
-#   prediction= "output/granie/prediction.csv",
-#   useWeightingLinks = FALSE,
-#   forceRerun = FALSE
-# )
-
+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"
 # )
-## VIASH END
+
 
 #### STANDARD ASSIGNMENTS ###
 file_seurat = "seurat_granie.qs"
@@ -210,11 +210,11 @@ 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
 )
 

diff --git a/src/methods/multi_omics/scglue_ns/config.vsh.yaml b/src/methods/multi_omics/scglue_ns/config.vsh.yaml
@@ -26,4 +26,4 @@ functionality:
 platforms:
   - type: nextflow
     directives:
-      label: [ midtime, midmem, lowcpu ]
+      label: [ hightime, midmem, lowcpu ]