fix errors in miRDeep2 analysis when reads map to unplaced contigs in $refgenome

[Daniel-VM]

This pull request attempts to fix a potential corner case in STEP 7.2 miRDeep2:

Some miRNA reads could map to unplaced contigs (ie: ">chr11_KI270721v1_random") in the reference genome
($refgenome). In such situation, removing "_" from the sequence ID of $refgenome leads to mismatch with
the chromosome IDs listed in the *.arf file ($reads_vs_refdb). Example:

    genome_nowhitespace.fa: >chr11KI270721v1random ($refgenome after removing underscore)
    $reads_vs_refdb: chr11_KI270721v1_random

Therefore, mirdeep2.pl doesn't identify the mapped read ($reads_vs_refdb) in the edited reference genome causing the following error:

""
Command error:
#Starting miRDeep2
[...]

The mapped reference id chr11_KI270721v1_random from file *_reads_vs_refdb.arf is
    not an id of the genome file genome_nowhitespace.fa
     [...]

""
PROPOSAL:

1. Avoid "_" removal with awk in STEP 7.2 miRDeep2
   In my case, this modification solves the above error.

2. if "_" is removed from $refgenome, then apply the same modification to the *.arf file in the $6 field (chromosome ID column) in order to preserve the chromosome's ID correspondence.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/smrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,conda).