BALSAMIC.commands.config package

Submodules

BALSAMIC.commands.config.base module

BALSAMIC.commands.config.case module

BALSAMIC.commands.config.case.check_exist(path)

Checks if fastq file readable and accessable.

BALSAMIC.commands.config.case.configure_fastq(fq_path, sample, fastq_prefix)

Configure the fastq files for analysis

BALSAMIC.commands.config.case.get_analysis_type(normal, umi)

return analysis type

BALSAMIC.commands.config.case.get_fastq_path(fq_file, fq_pattern)

BALSAMIC.commands.config.case.get_output_config(config, case_id)

return output config json file

BALSAMIC.commands.config.case.get_sample_config(sample_config, case_id, analysis_dir, analysis_type)

creating sample config to run the analysis

BALSAMIC.commands.config.case.link_fastq(src_files, des_path)

Creating fastq copy in given destination

BALSAMIC.commands.config.case.merge_json(*args)

Take a list of json files and merges them together

Input: list of json file Output: dictionary of merged json

BALSAMIC.commands.config.case.set_panel_bed(json_out, panel_bed)

Set panel path in config file

BALSAMIC.commands.config.reference module

Module contents