From a60f0ef8299fd5e8f22d30f7851d8e838b6d4b54 Mon Sep 17 00:00:00 2001 From: Jalil Nourisa Date: Sun, 15 Sep 2024 22:42:51 +0200 Subject: [PATCH] workflow updated --- src/methods/multi_omics/scglue/main.py | 6 ++++-- src/workflows/run_benchmark_single_omics/main.nf | 2 -- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py index 127a675f0..7e4c950b9 100644 --- a/src/methods/multi_omics/scglue/main.py +++ b/src/methods/multi_omics/scglue/main.py @@ -239,7 +239,7 @@ def prune_grn(par): par['genes_vs_motifs_500'] = 'output/scenic/databases/hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather' par['genes_vs_motifs_10k'] = 'output/scenic/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather' par['motif_annotation'] = 'output/scenic/databases/motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl' - + command = [ "pyscenic", "ctx", f"{par['temp_dir']}/draft_grn.csv", @@ -253,7 +253,9 @@ def prune_grn(par): "--nes_threshold", "2", "--mask_dropouts", "--min_genes", "1", - "--num_workers", f"{par['num_workers']}" + "--num_workers", f"{par['num_workers']}", + "--cell_id_attribute", "obs_id", + "--gene_attribute", "name" ] result = subprocess.run(command, check=True) diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf index db3349c5f..79030a692 100644 --- a/src/workflows/run_benchmark_single_omics/main.nf +++ b/src/workflows/run_benchmark_single_omics/main.nf @@ -18,8 +18,6 @@ workflow run_wf { genie3, grnboost2, ppcor, - scsgl, - tigress, scgpt, scenic ]