[bug] Poor quality / unmappeable samples cause snippy-core to fail with a confusing erorr message

[pvanheus]

Description
If a sample is poor quality or contains reads that don't map well against the reference, it will produce a very "gappy" alignment. Since snippy-core runs snp-sites -c it will exclude all sites where there is at least one gap in the column, which means that when a very gappy sample is included in the alignment, snp-sites -c will conclude that there are no variants in the alignment and snippy-core will crash (with the error message:

  Warning: No SNPs were detected so there is nothing to output.
  ERROR: Could not run: snp-sites -c -o core-snp.aln core-snp.full.aln

Steps to Reproduce

Given some samples that include either poor quality samples or perhaps samples that don't map well to this reference:

bactopia --wf cleanyerreads --samples sample_sheet.tsv --outdir cleaned_reads
bactopia --wf snippy --reference ref.genbank --bactopia cleaned_reads --run_name ref --outdir bactopia_snippy
[....]
  Warning: No SNPs were detected so there is nothing to output.
  ERROR: Could not run: snp-sites -c -o core-snp.aln core-snp.full.aln

Expected Behavior
The error here is actually in snippy-core so perhaps needs fixing upstream but bactopia could perhaps catch this error message and display more user friendly feedback (or use trimal -sident to identify poor candidates for inclusion in the alignment).

Execution Environment

• Bactopia Version: 3.0.0
• OS: Ubuntu 22.04
• Environment: slurm cluster with singularity

Additional Information
The upstream error comes from this part of snippy-core. This behaviour has led to at least one issue on the snippy Github: tseemann/snippy#434