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Preparation for "merge" viral pipeline into assembly pipeline

Martin Beracochea requested to merge preparation-for-merge into dev

Created by: KeteSakharova

The idea of these fixes is to rename contig headers to MGYPs that were assined in assembly pipeline.

Assembly pipeline will generate mapfile: digest(sequence) --> MGYP for already assigned proteins (that will also include FGS predictions).

New input params:

  • use_mgyp_from_assembly_pipeline (bool flag, default=false)
  • mapfile (from assembly pipeline)

If use_mgyp_from_assembly_pipeline set to true then prodigal sub-wf will use FastaRename subwf to rename headers.

I also added argument --proteins to FastaRename script. That will use similar procedure for renaming as we use for viral pipeline.

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