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

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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: 1525

Created: 7th Jul 2022 at 09:23

Last updated: 2nd Nov 2022 at 15:41

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