process multiomics updated

openproblems-bio · Nov 19, 2024 · 8b0ecf6 · 8b0ecf6
1 parent a3656b4
commit 8b0ecf6
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 48 deletions.
diff --git a/src/workflows/process_multiomics/config.vsh.yaml b/src/workflows/process_multiomics/config.vsh.yaml
@@ -27,16 +27,6 @@ functionality:
       direction: output
       example: resources/grn-benchmark/multiomics_atac.h5ad
 
-    - name: --multiomics_rna_d0_hvg
-      type: file 
-      required: false
-      direction: output
-      example: resources/grn-benchmark/multiomics_rna_d0_hvg.h5ad
-    - name: --multiomics_atac_d0
-      type: file 
-      required: false
-      direction: output
-      example: resources/grn-benchmark/multiomics_atac_d0.h5ad
 
     - name: --rna_rds
       type: file
@@ -49,17 +39,6 @@ functionality:
       direction: output
       example: resources/grn-benchmark/multiomics_atac.rds
 
-    - name: --rna_rds_d0_hvg
-      type: file
-      required: false
-      direction: output
-      example: resources/grn-benchmark/multiomics_rna_d0_hvg.rds
-    - name: --atac_rds_d0
-      type: file
-      required: false
-      direction: output
-      example: resources/grn-benchmark/multiomics_atac_d0.rds
-
   resources:
     - type: nextflow_script
       path: main.nf
@@ -68,7 +47,6 @@ functionality:
     - name: multiomics/format_data 
     - name: multiomics/multiome_matrix
     - name: multiomics/format_resources_r 
-    - name: multiomics/subset_hvg
 platforms:
   - type: nextflow
     directives:

diff --git a/src/workflows/process_multiomics/main.nf b/src/workflows/process_multiomics/main.nf
@@ -31,33 +31,8 @@ workflow run_wf {
                 atac_rds: "atac_rds"]
     )
 
-    | subset_hvg.run(
-      fromState: [multiomics_rna: "multiomics_rna", multiomics_atac: "multiomics_atac"],
-      toState: [multiomics_rna_d0_hvg: "multiomics_rna_d0_hvg", multiomics_atac_d0: "multiomics_atac_d0"]
-    )
-
-    | multiome_matrix.run(
-      fromState: [multiomics_rna: "multiomics_rna_d0_hvg", multiomics_atac: "multiomics_atac_d0"],
-      toState: [rna_matrix_d0: "rna_matrix",
-                atac_matrix_d0: "atac_matrix",
-                rna_gene_annot_d0: "rna_gene_annot",
-                rna_cell_annot_d0: "rna_cell_annot",
-                atac_peak_annot_d0: "atac_peak_annot",
-                atac_cell_annot_d0: "atac_cell_annot"]
-    )
-
-    | format_resources_r.run(
-      fromState: [rna_matrix: "rna_matrix_d0",
-                atac_matrix: "atac_matrix_d0",
-                rna_gene_annot: "rna_gene_annot_d0",
-                rna_cell_annot: "rna_cell_annot_d0",
-                atac_peak_annot: "atac_peak_annot_d0",
-                atac_cell_annot: "atac_cell_annot_d0"],
-      toState: [rna_rds_d0_hvg: "rna_rds",
-                atac_rds_d0: "atac_rds"]
-    )
 
-    | setState(["multiomics_rna", "multiomics_atac", "rna_rds", "atac_rds", "multiomics_rna_d0_hvg", "multiomics_atac_d0", "rna_rds_d0_hvg", "atac_rds_d0"])
+    | setState(["multiomics_rna", "multiomics_atac", "rna_rds", "atac_rds"])
 
   emit:
   output_ch