omicverse.alignment.fastp

omicverse.alignment.fastp(samples, output_dir='fastp', threads=8, jobs=None, max_workers=None, output_gzip=None, extra_args=None, fastp_path=None, auto_install=True, overwrite=False)[source]

Run fastp QC.

Parameters:

  • samples (Union[Tuple[str, str, Optional[str]], Sequence[Tuple[str, str, Optional[str]]]]) – (sample, fq1, fq2) tuple, list of such tuples, or a list of 1/2 FASTQ paths.

  • output_dir (str (default: 'fastp')) – Output directory for cleaned FASTQs (per-sample subdir).

  • threads (int (default: 8)) – Threads per fastp job.

  • jobs (Optional[int] (default: None)) – Concurrent jobs.

  • max_workers (Optional[int] (default: None)) – Legacy alias for jobs.

  • output_gzip (Optional[bool] (default: None)) – Force output gzip; None follows input fq1 suffix.

  • extra_args (Optional[Sequence[str]] (default: None)) – Additional fastp CLI arguments.

  • fastp_path (Optional[str] (default: None)) – Explicit path to fastp executable.

  • auto_install (bool (default: True)) – Install missing tools automatically when possible.

  • overwrite (bool (default: False)) – If True, rerun fastp and overwrite existing outputs.

Return type:

Union[Dict[str, str], List[Dict[str, str]]]