SwapConditional #

[[step]]
    action = "SwapConditional"
    in_label = "mytag"  # Boolean tag that determines whether to swap
    segment_a = "read1"       # Optional
    segment_b = "read2"       # Optional

Conditionally swaps exactly two segments based on a boolean tag value.

For each read, if the boolean tag is true, the segments are swapped for that specific read. If the tag is false, the read is left unchanged.

This is useful for conditionally reorganizing paired-end data based on read properties, such as swapping reads based on length, quality, or other criteria determined by prior steps.

Parameters #

• in_label: (required) The name of a boolean tag that determines whether to swap each read
• segment_a/segment_b: (optional) Only necessary if there are more than two segments defined in the input

Example #

# Create boolean tag: swap if read1 is longer than read2
[[step]]
    action = "EvalExpression"
    out_label = "swap_if_read1_longer"
    expression = "len_read1 > len_read2" # len_ tags are virtual
    result_type = "bool"

# Conditionally swap reads
[[step]]
    action = "SwapConditional"
    in_label = "swap_if_read1_longer"

Note that this does not reverse complement. You might want to use ReverseComplementConditional in conjunction.