diff --git a/smwrappers/explore_mapping_parameters/wrapper.py b/smwrappers/explore_mapping_parameters/wrapper.py index 334d0b5142c0fb70e2022a0d73245df4d206bdbe..90277fa52b33102f5ed19ff0fea9e69f4af7e906 100644 --- a/smwrappers/explore_mapping_parameters/wrapper.py +++ b/smwrappers/explore_mapping_parameters/wrapper.py @@ -55,12 +55,12 @@ echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rat return shell_commands with NamedTemporaryFile() as fastq, NamedTemporaryFile() as rates_record: - snakemake.params["fastq"] = fastq.name + snakemake.params.fastq = fastq.name # Take the first 10000 reads from the input shell(f"zcat {snakemake.input.fastq} | head -40000 | gzip > {fastq.name}") - snakemake.params["rates_record"] = rates_record.name + snakemake.params.rates_record = rates_record.name for settings in snakemake.params.settings: - snakemake.params["these_settings"] = settings + snakemake.params.these_settings = settings shell(mapping_command(snakemake.params.aligner)) rates_record.seek(0) (best_rate, best_settings) = max(