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Table 2 Executable pipelines for three usage scenarios

From: A graph-based approach for designing extensible pipelines

 File Code
 SDAT to R HierFstat
.inputs SDAT02
  SDAT202
.exec perl SDAT2Rhierfstat.pl SDAT02 SDAT202 RHierfstat02
.outputs RHierfstat02
 PolyPhred output to Structure
.inputs PolyOut01
.exec perl PolyPhred2PrettyBase.pl PolyOut01 PrettyBase01
  perl PrettyBase2SDAT.pl PrettyBase01 SDAT01
  perl SDAT2Structure.pl SDAT01 StructureFormat01 mainpar01 extrapar01
.outputs StructureFormat01
  mainparamt01
  extraparam01
 Phase to Fasta
.inputs PHASEOUT03
  Fragments03
  RefSeq03
.exec perl Phase2Fasta.pl PhaseOut03 Fragments03 RefSeq03 Fasta03
.outputs Fasta03
  1. Executable pipelines for file-format conversions: (top) SDAT format to R Hierfstat input format; (centre) PolyPhred output format to Structure input format; and (bottom) software PHASE output format to Fasta format. In practice, input and output files handled by the pipeline system are renamed to include a timestamp identifier of each specific pipeline (such as numbers 01, 02 and 03 above). This guarantees that inputs and outputs stored in the system are unique for each dynamically generated pipeline.