Fix `generate_args`

[zhuchcn]

Description

Sometimes arriba config parameters are not parsed to parseArriba in the correct order. Below is an example command, and for some reason the value for --min-confidence became 1, but it should be 'medium'.

moPepGen parseArriba \
    --input-path fusions.tsv \
    --index-dir index \
    --output-path ACH-000042_Fusion_Arriba.gvf \
    --source Fusion \
    --min-split-read2 1 \
    --min-confidence 1 \
    --min-split-read1 1

Closes #...

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