Inspect #

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

[[step]]
    action = "Inspect"
    n  = 1000 # how many molecules 
    infix = "inspect_at_point" # output filename infix
    segment = "read1" # Any of your input segments (use "all" for interleaved output)
    format = "FASTQ" # output format: FASTQ, FASTA or BAM
    suffix = "compressed" # (optional) custom suffix for filename
    compression = "gzip" # (optional) compression format: raw, gzip, zstd. Defaults to uncompressed
    compression_level = 1 # (optional) compression level for gzip/zstd/bam (gzip, zstd: 1-22)
                          # defaults: gzip=6, zstd=5

Output filename pattern:

• Without custom suffix:
  • When segment names a single read: {prefix}{ix_separator}{infix}{ix_separator}{segment}.{format_extension}
  • When segment = "all": {prefix}{ix_separator}{infix}{ix_separator}interleaved.{format_extension} (even if there’s only one segment present).
• With a custom suffix, replace {format_extension} with the explicit suffix (e.g. {prefix}{ix_separator}{infix}{ix_separator}{segment}.compressed).

Where {format_extension} is:

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

Note that inspect will collect all reads in memory before writing them out. When segment = "all" the collected reads are written in interleaved order (read1, read2, … per molecule).

All available tag data is automatically added to the read name.

Interaction with demultiplex #

Inspect does not create a file per demultiplex, it stores the demultiplex name as Demultiplex=~name~ in the read header line.