From 8b0ecf6751141e770ff1a010a26155f3d66f8073 Mon Sep 17 00:00:00 2001 From: Jalil Nourisa Date: Tue, 19 Nov 2024 13:26:48 +0100 Subject: [PATCH] process multiomics updated --- .../process_multiomics/config.vsh.yaml | 22 --------------- src/workflows/process_multiomics/main.nf | 27 +------------------ 2 files changed, 1 insertion(+), 48 deletions(-) diff --git a/src/workflows/process_multiomics/config.vsh.yaml b/src/workflows/process_multiomics/config.vsh.yaml index 3e30ecac6..28dac40b6 100644 --- 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 index 0e2e281d1..122b4c257 100644 --- 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