skills/pacsomatic/scripts/run_pacsomatic.py

• fail · function · L39-L41 — def fail(message)
• info · function · L44-L45 — def info(message)
• warn · function · L48-L49 — def warn(message)
• script_dir · function · L52-L53 — def script_dir()
• is_remote_path · function · L56-L58 — def is_remote_path(path)
• normalize_walltime_hhmmss · function · L61-L66 — def normalize_walltime_hhmmss(value, label)
• has_any_command · function · L69-L70 — def has_any_command(names)
• detect_java_major_version · function · L73-L81 — def detect_java_major_version()
• ensure_no_spaces · function · L84-L86 — def ensure_no_spaces(label, value)
• validate_repo · function · L89-L96 — def validate_repo(repo_path)
• ensure_pipeline_repo · function · L99-L124 — def ensure_pipeline_repo(args)
• parse_env_list_output · function · L127-L141 — def parse_env_list_output(raw_output, env_name)
• find_conda_env_prefix · function · L144-L158 — def find_conda_env_prefix(env_name)
• default_conda_env_file · function · L161-L162 — def default_conda_env_file()
• create_conda_env · function · L165-L180 — def create_conda_env(env_name, env_file)
• resolve_runtime · function · L183-L215 — def resolve_runtime(args)
• build_generated_params_content · function · L218-L227 — def build_generated_params_content(args, samplesheet_path)
• write_generated_params_file · function · L230-L235 — def write_generated_params_file(args, samplesheet_path)
• build_samplesheet · function · L238-L259 — def build_samplesheet(args, samplesheet_path)
• resolve_reference_args · function · L262-L267 — def resolve_reference_args(args)
• build_nextflow_command · function · L270-L305 — def build_nextflow_command(args, samplesheet_path)
• scheduler_header_lines · function · L308-L373 — def scheduler_header_lines(args)
• default_script_path · function · L376-L378 — def default_script_path(args)
• write_launch_script · function · L381-L414 — def write_launch_script(args, script_path, nextflow_cmd)
• verify_bam_and_index · function · L417-L435 — def verify_bam_and_index(label, bam_path, pbi_path)
• normalize_module_load · function · L445-L478 — def normalize_module_load(raw)
• validate_inputs · function · L481-L499 — def validate_inputs(args)
• ensure_runtime_tools · function · L502-L515 — def ensure_runtime_tools(args)
• ensure_dependency_tools · function · L518-L588 — def ensure_dependency_tools(args)
• submit_command_for_executor · function · L591-L605 — def submit_command_for_executor(executor, script_path)
• format_submit_command · function · L608-L613 — def format_submit_command(argv, stdin_path)
• extract_job_id · function · L616-L631 — def extract_job_id(executor, output)
• execute_launch · function · L634-L655 — def execute_launch(args, script_path)
• parse_args · function · L658-L736 — def parse_args()
• main · function · L739-L790 — def main()