diff --git a/src/base/labels_nebius.config b/src/base/labels_nebius.config index aa192a5ee..f670e1b61 100644 --- a/src/base/labels_nebius.config +++ b/src/base/labels_nebius.config @@ -74,7 +74,7 @@ process { // Nebius gpu-node-group: NVIDIA L40S, 1 GPU, 8 CPUs, 32 GiB RAM cpus = 6 accelerator = 1 - memory = 26.GB + memory = 100.GB disk = 200.GB pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00t775jb99svb7k5r']] containerOptions = { workflow.containerEngine == "singularity" ? '--nv': diff --git a/src/datasets/loaders/tenx_atera/script.py b/src/datasets/loaders/tenx_atera/script.py index 9532d049f..9aa4b4ed3 100644 --- a/src/datasets/loaders/tenx_atera/script.py +++ b/src/datasets/loaders/tenx_atera/script.py @@ -42,7 +42,12 @@ print(f"Extracting input zip to {tmpdirname}", flush=True) with zipfile.ZipFile(par_input, "r") as zip_ref: zip_ref.extractall(tmpdirname) - par_input = tmpdirname + # find the directory containing the Xenium output files (may be nested) + par_input = tmpdirname + for root, dirs, files in os.walk(tmpdirname): + if "cell_feature_matrix.h5" in files: + par_input = root + break # read the data sdata = xenium( diff --git a/src/datasets/loaders/tenx_xenium/script.py b/src/datasets/loaders/tenx_xenium/script.py index 3a3ee4633..c17e35cf5 100644 --- a/src/datasets/loaders/tenx_xenium/script.py +++ b/src/datasets/loaders/tenx_xenium/script.py @@ -42,7 +42,12 @@ print(f"Extracting input zip to {tmpdirname}", flush=True) with zipfile.ZipFile(par_input, "r") as zip_ref: zip_ref.extractall(tmpdirname) - par_input = tmpdirname + # find the directory containing the Xenium output files (may be nested) + par_input = tmpdirname + for root, dirs, files in os.walk(tmpdirname): + if "cell_feature_matrix.h5" in files: + par_input = root + break # read the data sdata = xenium(