Workflow Type: Common Workflow Language
Open
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 |
|
destination | Output Destination | Output destination used for cwl-prov reporting. |
|
eggnog_output | eggnog-mapper output | eggnog-mapper output file. Annotations tsv file (optional) |
|
embl_file | n/a | n/a |
|
genome_fasta | FASTA input file | Genome sequence in FASTA format |
|
identifier | Identifier | Identifier of the sample being converted |
|
interproscan_output | InterProScan output | InterProScan output file. JSON or TSV (optional) |
|
kofamscan_limit | SAPP kofamscan filter | Limit the number of hits per locus tag to be converted (0=no limit) (optional). Default 0 |
|
kofamscan_output | kofamscan output | KoFamScan / KoFamKOALA output file. detail-tsv (optional) |
|
threads | n/a | n/a |
|
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 |
|
Version History
Version 1 (earliest) Created 1st Oct 2024 at 14:46 by Bart Nijsse
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Created: 1st Oct 2024 at 14:46
Last updated: 3rd Oct 2024 at 10:43
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