Validate the S3 URIs in some delimited sample sheets actually exist

validate-remote-s3-paths.py

# After a `pip install sample-sheet pendant`

from sample_sheet import SampleSheet
from pendant.aws.s3 import S3Uri

def s3_validate_sample_sheet(path):
  for sample in SampleSheet(path):
      left = S3Uri(sample.PathToFastq1)
      right = S3Uri(sample.PathToFastq2)
      assert left.object_exists()
      assert right.object_exists()

def s3_validate_sample_merging_config(path):
  with open(path) as handle:
      next(handle)  # Consume the header
      for line in handle:
          sample, library, prefix = line.strip().split(',')
          assert S3Uri(f'{prefix}/{sample}.{library}/{sample}.{library}.raw.mapped.bam').object_exists()