Microbial Life History Traits

A new pipeline to identify microbial life history traits!
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Table of Contents

1. About The Project
2. Getting Started
   • Prerequisites
   • Usage
   • Parameters
   • Further recomendations
3. Citation

About the project

Getting started

Prerequisites

This pipeline requires the bellow software to be installed, please click on the icons for the installation instructions.

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Usage

To run this pipeline simply execute the following command. Additional parameters are described below.

nextflow run jotech/mlht

Parameters

--samples

The input file must be in csv format with two columns, specifying the id and the path to the assembly file. The first line of the file must be a header. You can find an example of the input file in assets/samples.csv. The following is an example of a valid input file:

id,file
SAM-ID,/path/to/assembly.fasta

It is important to note that the id must be unique and cannot contain spaces. The path to the assembly file could be a local file or a remote file (e.g. ftp, http, etc.)

Databases

The first time you run the pipeline it will download the required databases to a folder called dbs. Then, you can pass the databases as parameters to avoid the download step. This is how the databases are passed to the pipeline:

1. Bakta:

   --bakta_db ./dbs/bakta
   

2. Eggnog:

   --eggnog_db ./dbs/eggnog
   

3. Antismash:

   --antismash_db ./dbs/antismash
   

4. Platon:

   --platon_db ./dbs/platon
   

5. dbCAN:

   --dbcan_db ./dbs/dbcan
   

6. Kofamscan:

   --kofam_profiles ./dbs/kofam/profiles --kofam_ko_list ./dbs/kofam/ko_list
   

The dbs/ folder consist of symbolic links to the work/ folder. If you would like to delete work/ but keep the databases, you can do so by running the following command:

cp --dereference dbs/ hard_dbs/
rm -f work/ && rm -f dbs/ && mv hard_dbs/ dbs/

Further recommendations

It is often useful to cache the conda environment to avoid downloading the same packages multiple times. To do so, you can set the following environment variable:

export NXF_CONDA_CACHEDIR=/path/to/conda/environment/cache/directory/

Citation

If you use this pipeline please cite the following paper:

Zimmermann, J., Mendoza-Mejía N., et al. (2024). A new pipeline to identify microbial life history traits.

The paper is not yet published, please contact the authors of this repo for further information.