{"description": "Cell Ranger custom genome reference for read alignment and gene expression quantification", "assets": {"cellranger_reference": "ref"}, "required_files": [], "required_assets": [{"key": "gtf", "default": "gencode_gtf", "description": "Annotation file in Gene Transfer Format (GTF) from Gencode"}, {"key": "fasta", "default": "fasta", "description": "fasta asset for genome"}], "required_parameters": [{"key": "threads", "default": "8", "description": "Number of threads to use for parallel computing"}], "container": "databio/refgenie", "command_list": ["gunzip {gtf} -c > {asset_outfolder}/{genome}.gtf", "cellranger mkgtf {asset_outfolder}/{genome}.gtf {asset_outfolder}/{genome}_filtered.gtf", "rm {asset_outfolder}/{genome}.gtf", "cd {asset_outfolder}; cellranger mkref --genome=ref --fasta={fasta} --genes={asset_outfolder}/{genome}_filtered.gtf --nthreads={threads}"]}