Introduction

metaboflow is a bioinformatics pipeline that performs metabolic pathway profiling and functional annotation of microbial genomes and metagenome-assembled genomes (MAGs). It is built using Nextflow.

1. Gapseq pipeline for metabolic pathway profiling
2. GutSMASH for metabolic gene cluster detection
3. DRAM for functional annotation of metagenomes

Usage

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.

I recommend to perform assembly of metagenomic data and binning prior to running metaboflow. You can use e.g. the nf-core/mag pipeline for this purpose. The resulting bins (fasta files) can then be used as input for metaboflow.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

bin_id,bin_fasta,checkm_completeness,checkm_contamination
bin1,/path/to/bin1.fasta,95.0,2.0

Each row represents a bin.

Now, you can run the pipeline using:

nextflow run barbarahelena/metaboflow \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --gtdbtk_database </path/to/database> \
   --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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Credits

metaboflow was originally written by barbarahelena. I'm using different tools in this pipeline that you should cite if you use metaboflow in your research. Please see the CITATIONS.md file for more details.

Contributions and Support

If you would like to contribute to this pipeline, don't hesitate to get in touch.

Citations

This pipeline uses Gapseq, GutSMASH, DRAM and other tools. Please cite the respective publications when using this pipeline in your research.

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.