cellarr.slurm package¶

Submodules¶

cellarr.slurm.build_cellarr_steps module¶

class cellarr.slurm.build_cellarr_steps.SlurmBuilder(output_dir, log_dir, temp_dir, memory_gb=64, time_hours=24, cpus_per_task=4)[source]¶

Bases: object

SLURM-based builder for CellArrDataset.

__init__(output_dir, log_dir, temp_dir, memory_gb=64, time_hours=24, cpus_per_task=4)[source]¶

Initialize the SLURM builder.

Parameters:

output_dir (str) – Path to final output directory.
log_dir (str) – Path to store SLURM logs.
temp_dir (str) – Path for temporary files.
memory_gb (int) – Memory per job in GB.
time_hours (int) – Time limit per job in hours.
cpus_per_task (int) – CPUs per task.

create_array_script(job_name, python_script, args, n_tasks, dependencies=None, python_env='')[source]¶

Create a SLURM array job submission script.

Return type:: str

create_slurm_script(job_name, python_script, args, dependencies=None, python_env='')[source]¶

Create a SLURM job submission script.

Return type:: str

submit_cell_metadata_job(files, cell_options, dependency, python_env)[source]¶

Submit cell metadata processing job.

Return type:: str

submit_final_assembly(matrix_names, dependencies, python_env)[source]¶

Submit final assembly job.

Return type:: str

submit_gene_annotation_job(files, gene_options, python_env)[source]¶

Submit gene annotation processing job.

Return type:: str

submit_job(script_path)[source]¶

Submit a SLURM job and return job ID.

Return type:: str

submit_matrix_processing(files, matrix_options, dependency, python_env)[source]¶

Submit matrix processing as SLURM array job.

Return type:: Tuple[str, str]

submit_sample_metadata_job(files, sample_options, dependency, python_env)[source]¶

Submit sample metadata processing job.

Return type:: str

cellarr.slurm.build_cellarr_steps.main()[source]¶

cellarr.slurm.final_assembly module¶

cellarr.slurm.final_assembly.final_assembly(args_json)[source]¶

cellarr.slurm.finalize_matrix module¶

cellarr.slurm.finalize_matrix.finalize_matrix(args_json)[source]¶: Finalize the matrix after all array jobs complete.

cellarr.slurm.process_cell_metadata module¶

cellarr.slurm.process_cell_metadata.process_cell_metadata(args_json)[source]¶

Process and create cell metadata store.

Creates cell metadata including: - Sample mapping - Cell indices within samples - Original cell annotations from input files

cellarr.slurm.process_gene_annotation module¶

cellarr.slurm.process_gene_annotation.process_gene_annotation(args_json)[source]¶

cellarr.slurm.process_matrix module¶

cellarr.slurm.process_matrix.process_matrix_file(args_json)[source]¶: Process a single file for matrix creation.

cellarr.slurm.process_matrix_all module¶

cellarr.slurm.process_matrix_all.process_matrix(args_json)[source]¶

cellarr.slurm.process_sample_metadata module¶

cellarr.slurm.process_sample_metadata.process_sample_metadata(args_json)[source]¶

Process and create sample metadata store.

Creates sample metadata including: - Basic sample information - Cell counts per sample - Original gene sets - Sample index information