Re-write some parts to prevent code injection

[emarinier]

Currently, using echo to write possibly user-supplied filenames and sample ID fields might introduce a vulnerability to code injection. We should consider moving generate_summary to be after the IRIDA JSON output is produced and have it launch a Python process that reads the final JSON file, handles the data, and then writes the summary.txt.gz file.

[emarinier]

Also related: #9 (comment)

[emarinier]

Confirming that I was able do very basic code injection through the sample name provided in the samplesheet.

Ideas and recommendations for preventing code injection:

• Have nf-validation prevent certain characters (;,|,>,etc.)
• Scan parameters for special characters.
• Do not pass any user-modifiable fields into a bash command.