StoreTagInComment #

Store currently present tags as comments on read names.

[[step]]
    action = "StoreTagInComment"
    label = "mytag" # if set, only store this tag
    segment = "read1" # Any of your input segments, or 'All'
    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

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.

For example, a read name like:

@ERR12828869.501 A00627:18:HGV7TDSXX:3:1101:10502:5274/1

becomes:

@ERR12828869.501|key=value|key2=value2 A00627:18:HGV7TDSXX:3:1101:10502:5274/1

This way, your added tags will survive STAR alignment (STAR always cuts at the first space).