Workflow Type: Common Workflow Language
Open
Work-in-progress
Workflow for microbial (meta-)genome annotation
Input is a (meta)genome sequence in fasta format.
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bakta
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KoFamScan (optional)
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InterProScan (optional)
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eggNOG mapper (optional)
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To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub
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Inputs
ID | Name | Description | Type |
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threads | Number of threads | Number of threads to use for computational processes. Default 4 |
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genome_fasta | Genome fasta file | Genome fasta file used for annotation (required) |
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codon_table | Codon table | Codon table 11/4. Default = 11 |
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bakta_db | Bakta DB | Bakta database directory (default bakta-db_v5.1-light built in the container) (optional) |
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metagenome | metagenome | Run in metagenome mode. Affects only protein prediction. Default false |
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skip_bakta_plot | Skip plot | Skip Bakta plotting |
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skip_bakta_crispr | Skip bakta CRISPR array prediction using PILER-CR | Skip CRISPR prediction |
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interproscan_directory | InterProScan 5 directory | Directory of the (full) InterProScan 5 program. When not given InterProscan will not run. (optional) |
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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 |
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eggnog_dbs | n/a | n/a |
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run_kofamscan | Run kofamscan | Run with KEGG KO KoFamKOALA annotation. Default false |
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kofamscan_limit_sapp | SAPP kofamscan filter | Limit max number of entries of kofamscan hits per locus in SAPP. Default 5 |
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run_eggnog | Run eggNOG-mapper | Run with eggNOG-mapper annotation. Requires eggnog database files. Default false |
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run_interproscan | Run InterProScan | Run with eggNOG-mapper annotation. Requires InterProScan v5 program files. Default false |
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compress_output | n/a | Compress output files. Default false |
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sapp_conversion | n/a | Run SAPP (Semantic Annotation Platform with Provenance) on the annotations. Default true |
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destination | Output Destination (prov only) | Not used in this workflow. Output destination used in cwl-prov reporting only. |
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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 |
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compressed_other_files | n/a | n/a |
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uncompressed_other_files | n/a | n/a |
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sapp_hdt_file | n/a | n/a |
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Version History
Version 1 (earliest) Created 1st Oct 2024 at 14:16 by Bart Nijsse
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Created: 1st Oct 2024 at 14:16
Last updated: 3rd Oct 2024 at 10:47
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