Workflow Type: Common Workflow Language
Open
Work-in-progress
Workflow for microbial (meta-)genome annotation
Input is a (meta)genome sequence in fasta format.
-
bakta
-
KoFamScan (optional)
-
InterProScan (optional)
-
eggNOG mapper (optional)
-
To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
threads | Number of threads | Number of threads to use for computational processes. Default 4 |
|
genome_fasta | Genome fasta file | Genome fasta file used for annotation (required) |
|
codon_table | Codon table | Codon table 11/4. Default = 11 |
|
bakta_db | Bakta DB | Bakta database directory (default bakta-db_v5.1-light built in the container) (optional) |
|
metagenome | metagenome | Run in metagenome mode. Affects only protein prediction. Default false |
|
skip_bakta_plot | Skip plot | Skip Bakta plotting |
|
skip_bakta_crispr | Skip bakta CRISPR array prediction using PILER-CR | Skip CRISPR prediction |
|
interproscan_directory | InterProScan 5 directory | Directory of the (full) InterProScan 5 program. When not given InterProscan will not run. (optional) |
|
interproscan_applications | Interproscan applications | Comma separated list of analyses: FunFam,SFLD,PANTHER,Gene3D,Hamap,PRINTS,ProSiteProfiles,Coils,SUPERFAMILY,SMART,CDD,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite,PIRSF,NCBIfam default Pfam,SFLD,SMART,AntiFam,NCBIfam |
|
eggnog_dbs | n/a | n/a |
|
run_kofamscan | Run kofamscan | Run with KEGG KO KoFamKOALA annotation. Default false |
|
kofamscan_limit_sapp | SAPP kofamscan filter | Limit max number of entries of kofamscan hits per locus in SAPP. Default 5 |
|
run_eggnog | Run eggNOG-mapper | Run with eggNOG-mapper annotation. Requires eggnog database files. Default false |
|
run_interproscan | Run InterProScan | Run with eggNOG-mapper annotation. Requires InterProScan v5 program files. Default false |
|
compress_output | n/a | Compress output files. Default false |
|
sapp_conversion | n/a | Run SAPP (Semantic Annotation Platform with Provenance) on the annotations. Default true |
|
destination | Output Destination (prov only) | Not used in this workflow. Output destination used in cwl-prov reporting only. |
|
Steps
ID | Name | Description |
---|---|---|
bakta | Bakta | Bacterial genome annotation tool |
kofamscan | KofamScan | n/a |
interproscan | InterProScan 5 | n/a |
eggnogmapper | eggNOG-mapper | n/a |
compress_bakta | Compress Bakta | n/a |
compressed_other | Compressed other | Compress files when compression is true |
uncompressed_other | Uncompressed other | Gather files when compression is false |
workflow_sapp_conversion | n/a | n/a |
bakta_to_folder | Bakta to folder | Move all Bakta files to a folder |
Outputs
ID | Name | Description | Type |
---|---|---|---|
bakta_folder | n/a | n/a |
|
compressed_other_files | n/a | n/a |
|
uncompressed_other_files | n/a | n/a |
|
sapp_hdt_file | n/a | n/a |
|
Version History
Version 1 (earliest) Created 1st Oct 2024 at 14:16 by Bart Nijsse
Initial commit
Open
master
a39247f
Creators and Submitter
Creators
Submitter
Discussion Channel
License
Activity
Views: 387 Downloads: 122
Created: 1st Oct 2024 at 14:16
Last updated: 3rd Oct 2024 at 10:47
Annotated Properties
Topic annotations
Operation annotations
Attributions
None