Microbial (meta-) genome annotation
Version 1

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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

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SEEK ID: https://workflowhub.eu/workflows/1170?version=1

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
Creators
Submitter
Discussion Channel
https://gitlab.com/m-unlock/cwl/-/issues
License
Apache License 2.0
Activity

Views: 439   Downloads: 128

Created: 1st Oct 2024 at 14:16

Last updated: 3rd Oct 2024 at 10:47

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