Workflow Type: Common Workflow Language
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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 |
|
bins | Genome/bin | Bin/genome fasta files |
|
solver | n/a | Solver to be used in MEMOTE and SMETANA (defaul; cplex) |
|
threads | number of threads | Number of threads to use for computational processes |
|
destination | Output Destination (prov only) | Not used in this workflow. Output destination used for cwl-prov reporting only. |
|
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 |
|
protein_fasta_folder | Protein files folder | Prodigal predicted proteins (compressed) fasta files |
|
memote_folder | MEMOTE outputs folder | MEMOTE outputs folder |
|
smetana_output | SMETANA output | SMETANA detailed output table |
|
gemstats_out | GEMstats | CarveMe GEM statistics |
|
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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