Add sanity checks in order to prevent pipeline termination errors

[LordRust]

After running through 2000+ MRSA samples some exited with errors. Most of these can be prevented if the fastq files have some initial sanity checks and stops the isolate from further processing since the whole batch of samples stops when one error is encountered.

• SKESA exits with "Reads are too short for selected minimal kmer length" if the fastq files only have very short reads. Typically a failed sequencing, so in most cases it should be enough that the fastq files has some minimum number of reads.
• is the file that is referenced in the csv actually there? It might sound a bit to pedantic to check, but attached storage servers could be down, automated starts of analysis would fail if the demultiplexing does not result in a file for one sample in a run, etc.
• in some samples a trailing space had snuck into the "id" column of the csv. This crashes the pipeline at a later stage since it is not built to handle whitespace in filename. Chomping the whitespace in the ends of the id should be fine, because no one should sort files by leading trailing or leading whitespace (like my old colleague Flemming did).