Rename #

[[step]]
    action = "Rename"
    search = '(.)/([1/2])$'
    replacement = '$1 $2'

Apply a regular expression based renaming to the reads.

It is always applied to all available segments (read1, read2, index1, index2).

The example above fixes old school MGI reads for downstream processing, like fastp’s ‘–fix_mgi’ option

You can use the full power of the rust regex crate here.

Read index placeholder #

After the regex replacement runs, the special literal {{READ_INDEX}} is expanded to the running 1-based index of each logical read. When multiple segments are present (for example read1/read2 pairs), every segment for the same read receives the same index so pairs stay aligned. This makes it easy to re-sequence identifiers:

[[step]]
    action = "Rename"
    search = '^(.*)/(\d)$'
    replacement = 'LIB-{{READ_INDEX}}/$2'

The placeholder can appear multiple times within the replacement and is safe to mix with regex capture groups.