Input section #

[input]
    read1 = ['fileA_1.fastq', 'fileB_1.fastq.gz', 'fileC_1.fastq.zstd']
    read2 = ['fileA_1.fastq', 'fileB_1.fastq.gz', 'fileC_1.fastq.zstd'] # (optional)
    index1 = ['index1_A.fastq', 'index1_B.fastq.gz', 'index1_C.fastq.zstd'] # (optional)
    index2 = ['index2_A.fastq', 'index2_B.fastq.gz', 'index2_C.fastq.zstd'] # (optional)
    # but if index1 is set, index2 must be present as well
    interleaved = false # (optional) read1 is actually read1/2 interleaved. Read2 must not be set.
                        # Interleaved input needs twice as much memory than non-interleaved input.
                        # (We duplicate a whole block instead of allocating each read for performance reasons)

You can omit all inputs but read1.

Values may be lists or single filenames.

Compression is detected from file contents (.gz/bzip2/zstd).

Files must match, i.e. the first file in read1 must have the same number of reads (lines) as the first file in read2, etc.