Contaminant screening input -Add trim_only and raw options to --contaminant_screening_input #979

Job	Run time
Get Shards	19s
GPU Test \| singularity \| 1 \| 25.10.4 \| pipeline	6h 53m 8s
GPU Test \| docker \| 2 \| 25.10.4 \| pipeline	16m 54s
GPU Test \| docker \| 1 \| 25.10.4 \| pipeline	6h 53m 8s
GPU Test \| singularity \| 2 \| 25.10.4 \| pipeline	6h 53m 8s
confirm-pass-gpu	6s
GPU Test \| singularity \| 1 \| 25.10.4 \| pipeline	27m 34s
GPU Test \| docker \| 1 \| 25.10.4 \| pipeline	22m 21s
GPU Test \| singularity \| 2 \| 25.10.4 \| pipeline	21m 13s
GPU Test \| docker \| 2 \| 25.10.4 \| pipeline	16m 54s
Get Shards	19s
confirm-pass-gpu	6s
	22h 25m 10s

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