StoreTagInFastQ #

# Store the content of a tag in a fastq file.
# Needs a 'location 'tag'.
# Can store other tags in the read name.
# quality scores are set to '~'.
# With demultiplexing: creates separate files per barcode
 [[step]]
    action = "StoreTagInFastQ"
    in_label = "mytag" # tag to store. If no infix is set, infix = tag={in_label}
    format = "Fastq" # FASTQ / FASTA / BAm
    compression = "gz" # or "zstd" | "none" # (optional) compression format, not if format == BAM
    compression_level = 6 # (optional) compression level for gzip (0-9) or zstd (1-22)
   					  # defaults: gzip=6, zstd=5
    comment_tags = []# e.g. ["other_tag"] # see StoreTagInComment
    comment_location_tags = ["mytag"] # (optional) tags to add location info for, defaults to [in_label]
                                      # set to [] to disable location tracking
    comment_insert_char = ' ' # (optional) char at which to insert comments
    comment_separator = '|' # (optional) char to separate comments
    region_separator = "_" # (optional) char to separate regions in a tag, if it has multiple

Store the sequence of a tag in a fastq file, with other tags optionally stored in the read name as comments.

The output filename is constructed as {prefix}_tag.{label}.fq (or with custom separator if configured).

Comments are key=value pairs, separated by comment_separator which defaults to ‘|’. They get inserted at the first comment_insert_char, which defaults to space.

By default, location information is added to read names in the format {tag}_location=segment:start-end (e.g., barcode_location=read1:0-4). This can be controlled with comment_location_tags:

Defaults to [in_label] - adds location for the main tag
Set to [] to disable location tracking
Set to specific tag names to track locations for those tags only

Interaction with demultiplex #

When demultiplexing is used, separate FASTQ files are created for each barcode: {prefix}_{barcode}.tag.{label}.fq