OutputFASTA #

Write reads to FASTA file(s) as a pipeline step. Like OutputFASTQ but emits FASTA records (no quality line). This is the step-based equivalent of the legacy [output] section with format = "fasta".

[input]
    read1 = "input.fq"

[[step]]
    action = "OutputFASTA"
    output = ["read1"]            # segments to write to individual files (alias: segments). Defaults to all input segments.
    suffix = "fasta"              # (optional) override the file suffix
    compression = "Raw"           # Raw / Gzip / Zstd
    # compression_level = 6       # (optional) gzip 0-9, zstd 1-22
    compression_threads = 1       # compression worker threads
    stdout = false                # write a single interleaved stream to stdout
    # interleave = ["read1","read2"]  # segments to interleave into one file (alias: interleaved)
    # chunksize = 1000000         # (optional) split into chunks of N molecules
    output_hash_uncompressed = false  # write an uncompressed-content hash sidecar
    output_hash_compressed = false    # write a compressed-content hash sidecar

[output]
    prefix = "output"

Files are named like OutputFASTQ, but with the FASTA suffix. The output prefix is still taken from the [output] section.

Chunking #

When chunksize is set, start a new file every N molecules. File names will end on .%number%, left padded with zeros to the actual needed number of digits.