Update with significant software releases about pante2-legacy HOT 8 CLOSED

Error in mmseqs, new version input options. Updated as (removed --dont-split-seq-by-len)
https://github.com/KristinaGagalova/pante2/blob/0d9667a91134151c709e1339185e38c5c034ad8a/main.nf#L1433

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Error in tRNAscan

 tRNAscan-SE       -E       -o "A_fumigatus_A1163_chr1_chr2_trnascan.txt"       -f "A_fumigatus_A1163_chr1_chr2_trnascan_ss.txt"       -s "A_fumigatus_A1163_chr1_chr2_trnascan_iso.txt"       -m "A_fumigatus_A1163_chr1_chr2_trnascan_stats.txt"       -b "A_fumigatus_A1163_chr1_chr2_trnascan.bed"       -a "A_fumigatus_A1163_chr1_chr2_trnascan.fasta"       --forceow       --log trna.log       --thread "1"       "A_fumigatus_A1163_chr1_chr2.fasta"

Command exit status:
  2

Command output:
  (empty)

Command error:
  Unable to open /tmp/.tmpdir.51260915//tscan206255.fpass for writing.  Aborting program.

tmp directory has to be changed from the config file.

UPDATE:
THIS ONLY HAPPENS ON DUG - missing /tmp directory on the HPC system

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Will address #10 even if won't fix it with the old versions

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Updates on RepeatModeler (-pa option is not available anymore)
https://github.com/KristinaGagalova/pante2/blob/cef5f787e91e5464752b6524eaffabaf154eb724/main.nf#L1329

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Bio.Alphabet change - update of the script needed or roll back to another version. More details here

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

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Missing library to DECIPHER

Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
...

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Bio.Alphabet depreciated (see before)
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

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RepeatModeller 2.x.x does not have engine. The command needs to be updated

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