Inspect

Inspect #

Dump a few reads to a file for inspection at this point in the graph.

[[step]]
    action = "Inspect"
    n  = 1000 # how many reads
    infix = "inspect_at_point" # output filename infix
    segment = "read1" # Any of your input segments
    suffix = "compressed" # (optional) custom suffix for filename
    format = "gzip" # (optional) compression format: raw, gzip, zstd (defaults to raw)
    compression_level = 1 # (optional) compression level for gzip (0-9) or zstd (1-22)
                          # defaults: gzip=6, zstd=5

Output filename pattern:

  • Without custom suffix: {prefix}_{infix}_{segment}.{format_extension}
  • With custom suffix: {prefix}_{infix}_{segment}_{suffix}.{format_extension}

Where {format_extension} is:

  • fq for raw format
  • fq.gz for gzip format
  • fq.zst for zstd format

Note that inspect will collect all reads in memory before writing them out.