Clean up output from generate_logs.sh

[Nick-Eagles]

Currently, scripts/generate_logs.sh makes the assumption that all nextflow processes have completed (whether successfully or not). However, whenever the pipeline halts before completing (e.g. due to a temporary filesystem issue), some processes are typically killed mid-execution, leading to some files in some working directories being absent.

scripts/generate_logs.sh attempts to proceed, taking quite some time for larger experiments, and filling up the main log (`SPEAQeasy_output.log) with error messages such as:

cat: [insert work directory here]/.exitcode: No such file or directory

Instead, scripts/generate_logs.sh should properly handle missing files, possibly stating they are missing in the per-sample logs.

[gpertea]

I have just used a quick'n'clumsy patch for this in the jhpce_custom branch, see:
https://github.com/LieberInstitute/SPEAQeasy/blob/jhpce_custom/scripts/generate_logs.sh
.. maybe it could be fetched into master if you think it's acceptable.