Clean up WGS reports

[ewels]

For NGI plugin hooks:

• Collapse sample name to P123_001
• Remove lane level stats from General Stats table
  • FastQC
  • FastQ_Screen
• Throw a warning if suffix is not .clean, .clean.dedup or .clean.dedup.recal
  • Suffixes in a config file

Only do all of this if running on piper_ngi

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For NGI config file:

• Ignore folders
  • piper_ngi/01_raw_alignments
  • piper_ngi/02_preliminary_alignment_qc
  • piper_ngi/03_genotype_concordance
  • piper_ngi/04_merged_alignments

[ewels]

Note that some of these steps need to be in a hook before module execution (ignoring files) and some afterwards (general stats modification, sample name collapses)

[ewels]

Updated original issue comment to organise how to do this

[ewels]

..maybe better to use regex replace matching instead of this hardcoded approach? Will work in plots as well as general stats table then..

[ewels]

I think this is probably fine for now.