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Modify suffix of Prodigal outputs

Vini Salazar requested to merge vsalazar/metaGenePipe:prodigal-out into verbruggen

Hi,

I was encouraged to contribute to the code base so I hope you will find this small change useful :)

If merged, this PR will modify the suffix and extension of Prodigal output files.

Prodigal outputs four files: two sequence files (nucleotide and amino acid), a Genbank features file, and a coordinates file with scores of all potential genes. The latter two have specific extensions, that may be better than the current .fa extension which suggests that they are also sequence (FASTA-like) files.

Summary of changes:

  • Modify strings in 'output' key of prodigal_task.wdl
  • Modify 'command' key accordingly

Best,
Vini

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