From 21002ba8d149ba1270c153351098144dd52b437e Mon Sep 17 00:00:00 2001 From: LouisK92 Date: Wed, 10 Dec 2025 17:37:00 +0100 Subject: [PATCH 1/2] Make sure sc adata var names are unique --- src/data_processors/process_dataset/script.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/data_processors/process_dataset/script.py b/src/data_processors/process_dataset/script.py index b4e47808..de91da88 100644 --- a/src/data_processors/process_dataset/script.py +++ b/src/data_processors/process_dataset/script.py @@ -180,6 +180,9 @@ def subsample_adata_group_balanced(adata, group_key, n_samples, seed=0): if adata.n_obs > N_MAX_SC: adata = adata[subsample_adata_group_balanced(adata, "cell_type", N_MAX_SC, seed=0)] +# Make the single-cell data gene names unique +adata.var_names_make_unique() + # Subset single-cell and spatial data to shared genes sp_genes = sdata['transcripts']['feature_name'].unique().compute().tolist() sc_genes = adata.var["feature_name"].unique().tolist() From 9e30442e93ffb6b6fb3e5621c1ed23dde15905da Mon Sep 17 00:00:00 2001 From: LouisK92 Date: Wed, 10 Dec 2025 17:44:04 +0100 Subject: [PATCH 2/2] Adjust memory and time --- src/methods_cell_type_annotation/ssam/config.vsh.yaml | 2 +- .../gene_efficiency_correction/config.vsh.yaml | 2 +- src/metrics/similarity/config.vsh.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/methods_cell_type_annotation/ssam/config.vsh.yaml b/src/methods_cell_type_annotation/ssam/config.vsh.yaml index cbd97dab..85319fa1 100644 --- a/src/methods_cell_type_annotation/ssam/config.vsh.yaml +++ b/src/methods_cell_type_annotation/ssam/config.vsh.yaml @@ -36,4 +36,4 @@ runners: - type: executable - type: nextflow directives: - label: [ hightime, midcpu, midmem ] \ No newline at end of file + label: [ veryhightime, midcpu, midmem ] \ No newline at end of file diff --git a/src/methods_expression_correction/gene_efficiency_correction/config.vsh.yaml b/src/methods_expression_correction/gene_efficiency_correction/config.vsh.yaml index 9fffd2c8..1d813fbd 100644 --- a/src/methods_expression_correction/gene_efficiency_correction/config.vsh.yaml +++ b/src/methods_expression_correction/gene_efficiency_correction/config.vsh.yaml @@ -38,4 +38,4 @@ runners: - type: executable - type: nextflow directives: - label: [ midtime, lowcpu, lowmem ] \ No newline at end of file + label: [ midtime, lowcpu, midmem ] \ No newline at end of file diff --git a/src/metrics/similarity/config.vsh.yaml b/src/metrics/similarity/config.vsh.yaml index 7a8dde9b..79faa93b 100644 --- a/src/metrics/similarity/config.vsh.yaml +++ b/src/metrics/similarity/config.vsh.yaml @@ -101,4 +101,4 @@ runners: # Allows turning the component into a Nextflow module / pipeline. - type: nextflow directives: - label: [midtime, highmem, midcpu] + label: [midtime, veryhighmem, midcpu]