From 6438b08d3a6308b84e3588592e060be0149cba5f Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Tue, 23 Jun 2026 22:53:49 +0200 Subject: [PATCH 1/3] fix processing --- 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 5976079d..533a0c7f 100644 --- a/src/data_processors/process_dataset/script.py +++ b/src/data_processors/process_dataset/script.py @@ -251,6 +251,9 @@ def subsample_adata_group_balanced(adata, group_key, n_samples, seed=0): filter_table=True, ) rechunk_sdata(sdata_output) #NOTE: rechunking currently needed (https://github.com/scverse/spatialdata/issues/929) + # metadata is dataset-level, not spatial — re-add it if the bounding_box query dropped it + if "metadata" in sdata.tables and "metadata" not in sdata_output.tables: + sdata_output["metadata"] = sdata.tables["metadata"] else: sdata_output = sdata From da648f63c158d8f69383e9ebe9dcc3ecb2a8bed4 Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Tue, 23 Jun 2026 22:54:06 +0200 Subject: [PATCH 2/3] adjust link --- scripts/create_resources/spatial/process_10x_atera_nebius.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_resources/spatial/process_10x_atera_nebius.sh b/scripts/create_resources/spatial/process_10x_atera_nebius.sh index baf016a0..d3475e58 100644 --- a/scripts/create_resources/spatial/process_10x_atera_nebius.sh +++ b/scripts/create_resources/spatial/process_10x_atera_nebius.sh @@ -14,7 +14,7 @@ cat > /tmp/params_atera.yaml << HERE param_list: - id: "10x_atera/2026_10x_human_breast_cancer_atera" - input: https://s3-us-west-2.amazonaws.com/10x.files/samples/atera/dev/WTA_Preview_FFPE_Breast_Cancer/WTA_Preview_FFPE_Breast_Cancer_xe_outs.zip + input: https://s3-us-west-2.amazonaws.com/10x.files/samples/atera/dev/WTA_Preview_FFPE_Breast_Cancer/WTA_Preview_FFPE_Breast_Cancer_outs.zip dataset_name: "Atera WTA FFPE Human Breast Cancer" dataset_url: "https://www.10xgenomics.com/datasets/atera-wta-ffpe-human-breast-cancer" dataset_summary: "Preview dataset showcasing the pre-commercial Atera Whole Transcriptome Assay (WTA) applied to FFPE human breast cancer tissue, profiling 18,028 genes and detecting 170,057 cells." From a7ddc04223512c5f41d75bf1e07300c2d6c8f1de Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Tue, 23 Jun 2026 22:54:32 +0200 Subject: [PATCH 3/3] adjust memory --- src/datasets/workflows/process_tenx_atera/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/workflows/process_tenx_atera/config.vsh.yaml b/src/datasets/workflows/process_tenx_atera/config.vsh.yaml index 5b43ab44..58148a02 100644 --- a/src/datasets/workflows/process_tenx_atera/config.vsh.yaml +++ b/src/datasets/workflows/process_tenx_atera/config.vsh.yaml @@ -82,4 +82,4 @@ dependencies: runners: - type: nextflow directives: - label: [highcpu, midmem, hightime] \ No newline at end of file + label: [highcpu, highmem, hightime] \ No newline at end of file