Add checkIfExists to file inputs and fix S3 index validation #39

Job	Run time
nf-test-changes	1m 52s
singularity \| latest-everything \| 1/7	1m 56s
conda \| 25.04.0 \| 1/7	2m 17s
singularity \| 25.04.0 \| 1/7	2m 19s
singularity \| 25.04.0 \| 3/7	2m 17s
docker \| latest-everything \| 1/7	2m 13s
docker \| 25.04.0 \| 1/7	2m 18s
singularity \| latest-everything \| 2/7	2m 5s
conda \| latest-everything \| 1/7	2m 0s
conda \| latest-everything \| 2/7	1m 52s
singularity \| 25.04.0 \| 2/7	2m 20s
conda \| latest-everything \| 3/7	2m 20s
conda \| latest-everything \| 5/7	2m 20s
conda \| 25.04.0 \| 3/7	2m 9s
singularity \| 25.04.0 \| 6/7	2m 15s
docker \| latest-everything \| 2/7	1m 57s
docker \| latest-everything \| 6/7	2m 6s
conda \| 25.04.0 \| 2/7	2m 11s
docker \| 25.04.0 \| 2/7	2m 15s
singularity \| latest-everything \| 4/7	2m 4s
singularity \| latest-everything \| 5/7	2m 11s
docker \| 25.04.0 \| 6/7	1m 55s
conda \| 25.04.0 \| 5/7	2m 16s
conda \| 25.04.0 \| 4/7	2m 12s
docker \| latest-everything \| 7/7	2m 13s
docker \| latest-everything \| 5/7	2m 6s
docker \| latest-everything \| 3/7	2m 7s
singularity \| latest-everything \| 7/7	2m 10s
docker \| 25.04.0 \| 3/7	1m 59s
conda \| latest-everything \| 6/7	1m 57s
singularity \| 25.04.0 \| 4/7	1m 52s
docker \| 25.04.0 \| 5/7	2m 7s
docker \| latest-everything \| 4/7	2m 1s
singularity \| latest-everything \| 3/7	2m 1s
singularity \| 25.04.0 \| 5/7	2m 16s
conda \| latest-everything \| 7/7	1m 52s
singularity \| latest-everything \| 6/7	1m 58s
conda \| latest-everything \| 4/7	2m 4s
docker \| 25.04.0 \| 4/7	1m 58s
conda \| 25.04.0 \| 7/7	1m 59s
conda \| 25.04.0 \| 6/7	1m 54s
singularity \| 25.04.0 \| 7/7	2m 3s
docker \| 25.04.0 \| 7/7	2m 15s
confirm-pass	6s
	1h 30m 38s

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