Improve S3 error recognition for download (And also in general)

[dankwart-de]

I think for the S3 helper, there are two cases:

1. The application stops without an exit code => Thus all is fine, because the file was downloaded completely.
2. The application stops with an error! In this case, we need to check, if the amount of read records equals the amount of requested records. If this condition applies, all is good.

[vinjana]

In the spirit of defensive programming, file sizes should always get checked (i.e. was the FASTQ read completely from the S3 source). A filesize check is probably cheap but could protect against programming errors.