mag-genome-annotation-parallel/main
v0.1

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Workflow Type: Galaxy

This workflow performs automated, parallel annotation of metagenome-assembled genomes (MAGs) to generate standardized annotation outputs, merged summary tables, and integrated quality reports across all genomes.

SEEK ID: https://workflowhub.eu/workflows/2115?version=1

Inputs

ID Name Description Type
AMRFinderPlus database AMRFinderPlus database Select a database to annotate AMR genes with Bakta.
  • string
Bacterial Genomes Bacterial Genomes Input a collection with bacterial genomes
  • File[]
Bacterial genome annotation database Bacterial genome annotation database Select a database to predict CDS and small proteins (sORF) with Bakta.
  • string
Plasmid detection database Plasmid detection database Select a database to identify plasmids with PlasmidFinder.
  • string
Run Bakta Run Bakta Choose if you want to run bakta or not (can take a long time)
  • boolean

Steps

ID Name Description
5 Bacterial Genome Annotation - IWC n/a
6 Remove variable # toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
7 Format Bakta output toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
8 Merge PlasmidFinder toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
9 Remove beginning # toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
10 Convert to TAB separator Convert characters1
11 Merge Bakta Output toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
12 Convert space to TAB separator Convert characters1
13 Merge Integron Finder toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
14 Merge ISEScan toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
15 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0

Outputs

ID Name Description Type
PlasmidFinder Merged Summary PlasmidFinder Merged Summary n/a
  • File
bakta cut annotation summary bakta cut annotation summary n/a
  • File
Integron Finder Merged Output Integron Finder Merged Output n/a
  • File
ISEScan Merged Output ISEScan Merged Output n/a
  • File
multiqc html report multiqc html report n/a
  • File

Version History

v0.1 (earliest) Created 20th Mar 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 a6f83c3
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License
MIT License (MIT)
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Views: 258   Downloads: 1189   Runs: 0

Created: 20th Mar 2026 at 03:01

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