Microbial (meta-) genome annotation
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow for microbial (meta-)genome annotation

Input is a (meta)genome sequence in fasta format.

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

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
  • int?
genome_fasta Genome fasta file Genome fasta file used for annotation (required)
  • File
codon_table Codon table Codon table 11/4. Default = 11
  • int
bakta_db Bakta DB Bakta database directory (default bakta-db_v5.1-light built in the container) (optional)
  • Directory?
metagenome metagenome Run in metagenome mode. Affects only protein prediction. Default false
  • boolean
skip_bakta_plot Skip plot Skip Bakta plotting
  • boolean
skip_bakta_crispr Skip bakta CRISPR array prediction using PILER-CR Skip CRISPR prediction
  • boolean
interproscan_directory InterProScan 5 directory Directory of the (full) InterProScan 5 program. When not given InterProscan will not run. (optional)
  • Directory?
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
  • string
eggnog_dbs n/a n/a
  • record containing
    • Directory?
    • File?
    • File?
run_kofamscan Run kofamscan Run with KEGG KO KoFamKOALA annotation. Default false
  • boolean
kofamscan_limit_sapp SAPP kofamscan filter Limit max number of entries of kofamscan hits per locus in SAPP. Default 5
  • int?
run_eggnog Run eggNOG-mapper Run with eggNOG-mapper annotation. Requires eggnog database files. Default false
  • boolean
run_interproscan Run InterProScan Run with eggNOG-mapper annotation. Requires InterProScan v5 program files. Default false
  • boolean
compress_output n/a Compress output files. Default false
  • boolean
sapp_conversion n/a Run SAPP (Semantic Annotation Platform with Provenance) on the annotations. Default true
  • boolean
destination Output Destination (prov only) Not used in this workflow. Output destination used in cwl-prov reporting only.
  • string?

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
  • Directory
compressed_other_files n/a n/a
  • File[]
uncompressed_other_files n/a n/a
  • File[]?
sapp_hdt_file n/a n/a
  • File?

Version History

Version 1 (earliest) Created 1st Oct 2024 at 14:16 by Bart Nijsse

Initial commit


Open master a39247f
help Creators and Submitter
Activity

Views: 56   Downloads: 54

Created: 1st Oct 2024 at 14:16

Last updated: 3rd Oct 2024 at 10:47

Annotated Properties
Topic annotations
Operation annotations
help Attributions

None

Total size: 112 KB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH