Metagenomic GEMs from Assembly
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow for Metagenomics from bins to metabolic models (GEMs)

Summary

  • Prodigal gene prediction
  • CarveMe genome scale metabolic model reconstruction
  • MEMOTE for metabolic model testing
  • SMETANA Species METabolic interaction ANAlysis

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here:
Tools: https://gitlab.com/m-unlock/cwl
Workflows: https://gitlab.com/m-unlock/cwl/workflows

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Click and drag the diagram to pan, double click or use the controls to zoom.

Inputs

ID Name Description Type
identifier Identifier used Identifier for this dataset used in this workflow
  • string
bins Genome/bin Bin/genome fasta files
  • File[]
solver n/a Solver to be used in MEMOTE and SMETANA (defaul; cplex)
  • string
threads number of threads Number of threads to use for computational processes
  • int?
destination Output Destination (prov only) Not used in this workflow. Output destination used for cwl-prov reporting only.
  • string?

Steps

ID Name Description
prodigal prodigal prodigal gene/protein prediction
compress_prodigal Compress proteins Compress prodigal protein files
carveme CarveMe Genome-scale metabolic models reconstruction with CarveMe
compress_carveme Compress GEM Compress CarveMe GEM
gemstats GEM stats CarveMe GEM statistics
smetana SMETANA Species METabolic interaction ANAlysis
memote_report_snapshot MEMOTE report snapshot Take a snapshot of a model's state and generate a report.
memote_run MEMOTE report snapshot MEMOTE run analsis
carveme_files_to_folder CarveMe GEMs to folder Preparation of workflow output files to a specific output folder
prodigal_files_to_folder Prodigal proteins to folder Preparation of workflow output files to a specific output folder
memote_files_to_folder MEMOTE output Preparation of workflow output files to a specific output folder

Outputs

ID Name Description Type
carveme_gems_folder CarveMe GEMs folder CarveMe metabolic models folder
  • Directory
protein_fasta_folder Protein files folder Prodigal predicted proteins (compressed) fasta files
  • Directory
memote_folder MEMOTE outputs folder MEMOTE outputs folder
  • Directory
smetana_output SMETANA output SMETANA detailed output table
  • File
gemstats_out GEMstats CarveMe GEM statistics
  • File

Version History

Version 1 (earliest) Created 7th Jul 2022 at 09:23 by Bart Nijsse

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Views: 2067   Downloads: 193

Created: 7th Jul 2022 at 09:23

Last updated: 2nd Nov 2022 at 15:41

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