granie edited

src/api/comp_method_r.yaml

@@ -0,0 +1,38 @@
+functionality:
+  namespace: "methods_r"
+  info:
+    type: methods_r
+    type_info:
+      label: Method r
+      summary: A GRN inference method
+      description: |
+        A method for inferring GRN from expression data.
+  arguments:
+    - name: --multiomics_rna
+      type: file
+      required: false
+      direction: input
+      default: resources_test/grn-benchmark/multiomics_rna.rds
+    - name: --multiomics_atac
+      type: file
+      required: false
+      direction: input
+      default: resources_test/grn-benchmark/multiomics_atac.rds
+    - name: --prediction
+      __merge__: file_prediction.yaml
+      required: false
+      direction: output
+      default: output/grn.csv
+    - name: --temp_dir
+      type: string
+      direction: input
+      default: output/temdir
+    - name: --num_workers
+      type: integer
+      direction: input
+      default: 4
+  test_resources:
+    - type: python_script
+      path: /src/common/component_tests/run_and_check_output.py
+    - path: /resources/grn-benchmark
+      dest: resources/grn-benchmark

src/methods/multi_omics/granie/config.vsh.yaml

@@ -1,4 +1,4 @@
-__merge__: ../../../api/comp_method.yaml
+__merge__: ../../../api/comp_method_r.yaml
 
 
 functionality:
@@ -11,20 +11,6 @@ functionality:
       GRN inference using GRaNIE
     documentation_url: https://grp-zaugg.embl-community.io/GRaNIE/
   arguments:
-  - name: --file_rna
-    type: file
-    required: false
-    direction: input
-    description: "Path to the RNA data file (e.g., 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_r/atac.rds
-
   - name: --normRNA
     type: string
     required: false

src/methods/multi_omics/granie/script.R

@@ -101,12 +101,12 @@ if (!file.exists(file_RNA)) {
 if (par$forceRerun | !file.exists(file_seurat)) {
 
  # Sparse matrix
- rna.m = readRDS(par$file_rna)
+ rna.m = readRDS(par$perturbation_rna)
 
  seurat_object <- CreateSeuratObject(count = rna.m, project = "PBMC", min.cells = 1, min.features = 1, assay = "RNA")
 
  # RangedSummarizedExperiment
- atac = readRDS(par$file_atac)
+ atac = readRDS(par$perturbation_atac)
 
  # Extract counts and metadata from the RangedSummarizedExperiment
   atac_counts <- assays(atac)$counts

src/methods/multi_omics/granie_ns/config.vsh.yaml

@@ -0,0 +1,21 @@
+
+__merge__: ../../../api/comp_method.yaml
+
+functionality:
+  name: grn_inference_granie
+  namespace: "workflows"
+  info:
+    label: grn_inference_granie
+    summary: "Infers GRNs from multiomics data using granie."
+
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/granie 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [ hightime, midmem, highcpu ]

src/methods/multi_omics/granie_ns/main.nf

@@ -0,0 +1,21 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    | granie.run(
+      fromState: [
+              multiomics_rna: "multiomics_rna",
+              multiomics_atac: "multiomics_atac",
+              num_workers: "num_workers"
+              ],
+      toState: [prediction:"prediction"]
+    )
+
+    | setState(["prediction"])
+
+  emit:
+  output_ch
+}

src/methods/multi_omics/granie_ns/run.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+RUN_ID="scglue"
+resources_dir="s3://openproblems-data/resources/grn"
+publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
+
+num_workers=20
+
+param_file="./params/${RUN_ID}.yaml"
+
+cat > $param_file << HERE
+param_list:
+  - id: ${RUN_ID}
+    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
+    multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
+    annotation_file: ${resources_dir}/supplementary/gencode.v45.annotation.gtf.gz
+    motif_file: ${resources_dir}/supplementary/JASPAR2022-hg38.bed.gz
+    num_workers: $num_workers
+    temp_dir: ./tmp/grn
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+
+
+./tw-windows-x86_64.exe launch `
+       https://github.com/openproblems-bio/task_grn_benchmark.git `
+       --revision build/main `
+       --pull-latest `
+       --main-script target/nextflow/workflows/grn_inference_scglue/main.nf `
+       --workspace 53907369739130 `
+       --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+       --params-file ./params/scglue.yaml `
+       --config src/common/nextflow_helpers/labels_tw.config