YAML Parameters#

Required:

  • input_dir: Path to the input directory. Defaults to input if not specified.

  • output_dir: Path to the output directory. Defaults to output if not specified.

  • file_format: bed.gz, frag.gz, bam, or cram indicating the format of the input files. Defaults to bed.gz if not specified.

Optional:

  • supplement_dir: Path to supplemental files directory. Defaults to supplement if not specified.

  • mappability_file: Name of the bigWig mappability file in supplement_dir.

  • mappability_threshold: Minimum average mappability score (0.0-1.0) for interval filtering.

  • interval_file: Path to interval file in supplement_dir.

  • finaletoolkit_command: True/False: Enables a specific Finaletoolkit command, using hyphens replaced by underscores (e.g., adjust-wps becomes adjust_wps: True).

  • finaletoolkit_command_flag: value: Sets flags for a Finaletoolkit command (e.g., adjust_wps_max_length: 250). Flags that take input files, output files, or verbose flags do not exist here. mapping_quality is shortened to mapq for flags (e.g., coverage_mapping_quality becomes coverage_mapq).

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