precellar.utils.merge_fastq_files#

precellar.utils.merge_fastq_files(input1_files, output1_file, barcode_file, input2_files=None, output2_file=None, *, compression=None, compression_level=None, num_threads=4, verbose=False)#

Merge multiple FASTQ files into a single output file and generate a barcode file.

Parameters:

  • input1_files (list[str]) – List of paths to the first read (R1) FASTQ files.

  • input2_files (list[str] | None) – Optional list of paths to the second read (R2) FASTQ files.

  • output1_file (str) – Path to the output file for merged R1 reads.

  • output2_file (str | None) – Optional path to the output file for merged R2 reads.

  • barcode_file (str) – Path to the output barcode file.

  • compression (Literal['gzip', 'zst'] | None) – Compression algorithm to use. If None, the compression algorithm will be inferred from the file extension.

  • compression_level (int | None) – Compression level to use.

  • num_threads (int) – Number of threads to use for compression.

  • verbose (bool) – Controls the amount of output information.

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