SAPP conversion Workflow
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow for converting (genome) annotation tool output into a GBOL RDF file (TTL/HDT) using SAPP

Current formats / tools:

  • EMBL format
  • InterProScan (JSON/TSV)
  • eggNOG-mapper (TSV)
  • KoFamScan (TSV)

git: https://gitlab.com/m-unlock/cwl

SAPP (Semantic Annotation Platform with Provenance):
https://gitlab.com/sapp
https://academic.oup.com/bioinformatics/article/34/8/1401/4653704

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Inputs

ID Name Description Type
codon_table Codon table The codon table used for gene prediction
  • int
destination Output Destination Output destination used for cwl-prov reporting.
  • string
eggnog_output eggnog-mapper output eggnog-mapper output file. Annotations tsv file (optional)
  • File
embl_file n/a n/a
  • File
genome_fasta FASTA input file Genome sequence in FASTA format
  • File
identifier Identifier Identifier of the sample being converted
  • string
interproscan_output InterProScan output InterProScan output file. JSON or TSV (optional)
  • File
kofamscan_limit SAPP kofamscan filter Limit the number of hits per locus tag to be converted (0=no limit) (optional). Default 0
  • int
kofamscan_output kofamscan output KoFamScan / KoFamKOALA output file. detail-tsv (optional)
  • File
threads n/a n/a
  • int

Steps

ID Name Description
compress_hdt n/a n/a
embl_conversion n/a n/a
genome_conversion n/a n/a
sapp_eggnog n/a n/a
sapp_interproscan n/a n/a
sapp_kofamscan n/a n/a
turtle_to_hdt n/a n/a

Outputs

ID Name Description Type
hdt_file n/a Output directory
  • File

Version History

Version 1 (earliest) Created 1st Oct 2024 at 14:46 by Bart Nijsse

Initial commit


Open master e86ff84
help Creators and Submitter
Activity

Views: 519   Downloads: 81

Created: 1st Oct 2024 at 14:46

Last updated: 3rd Oct 2024 at 10:43

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