Rename reference to fasta in all cases

[apeltzer]

This should address the error in #130 and your issues @jfy133 :-)

Automatically renames any --fasta reference genome to use the *.fasta file extension if its not present already 👍

[jfy133]

This fixes the indexing issue - but downstream there a couple of places where the pipeline crashes, such as damageprofiler.

Maybe do a scan of anywhere else a fasta channel is used (e.g. possibly DamageProfiler and PMDtools - as based on line 242, for example.

Error where I discovered the issue:

ERROR ~ Error executing process > 'damageprofiler (ABM006.A0101_S0_L002_R1_001.sorted)'

Caused by:
  Missing output file(s) `*/*.json` expected by process `damageprofiler (ABM006.A0101_S0_L002_R1_001.sorted)`

Command executed:

  damageprofiler -i ABM006.A0101_S0_L002_R1_001.sorted.bam -r Tannerella_forsythia_9212.fa -l 100 -t 15 -o .

Command exit status:
  0

Command output:
  DamageProfiler v0.3.9

Work dir:
  /projects1/users/fellows/nextflow/eager2/dev_testing/eager2/01-actual_reference/tannerella_forsythia/Multiple/work/83/a9d4770fda4a5d6c473f92618be07d

[apeltzer]

Its an outdated environment in this case - can you download a new singularity container?

[apeltzer]

(new version should be DamageProfiler 0.4+, that can write out JSON log files, required for multiQC).