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 '~'.
# [[step]]
# action = "StoreTagInFastQ"
# label = "mytag" # ${output.prefix}.tag.mytag.fq${.suffix_from_format}
# format = "Raw" # Raw, Gzip, Zstd
## 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 [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.
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
[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