opencobra/jeweler is a bioinformatics pipeline that tests and grades genome-scale metabolic models (GEMs). It first validates SBML documents that describe metabolic models for constraint-based analysis. Valid documents are then passed on to the genome-scale metabolic model test suite (MEMOTE).
- Optionally, attempt to download an SBML document from a given model identifier (COBRApy).
- Validate the SBML document for use with constraint-based analysis (COBRApy).
- Test the model in the SBML document with the genome-scale metabolic model test suite (MEMOTE).
Note
If you are new to Nextflow and nf-core, please refer to this page on how
to set-up Nextflow. Make sure to test your setup
with -profile test before running the workflow on actual data.
Important
Currently, only a Docker image and a conda environment definition exist. Thus, only the options -profile docker or -profile conda are guaranteed to succeed.
First, prepare a samplesheet with your input data that looks as follows. Please also take a look at the test samplesheet for inspiration.
samplesheet.csv:
id,name,model
MODEL1507180060,iJR904,
MODEL2109130006,,
If the SBML document exists in an online repository, such as BioModels or BiGG, then the model identifier is enough. Otherwise, you need to reference the model file directly. An entry for the name is entirely optional.
Now, you can run the pipeline using:
nextflow run opencobra/jeweler \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those
provided by the -c Nextflow option can be used to provide any configuration except for parameters;
see docs.
opencobra/jeweler was originally written by Moritz E. Beber.
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use opencobra/jeweler for your analysis, please cite it using the following doi: 10.5281/zenodo.10173259.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.