Add trim_only and raw options to --contaminant_screening_input #967

Job	Run time
Get Shards	23s
GPU Test \| docker \| 1 \| 25.10.4 \| pipeline	22m 12s
GPU Test \| docker \| 2 \| 25.10.4 \| pipeline	16m 9s
GPU Test \| singularity \| 2 \| 25.10.4 \| pipeline	21m 53s
GPU Test \| singularity \| 1 \| 25.10.4 \| pipeline	26m 44s
confirm-pass-gpu	5s
	1h 27m 26s

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