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Usage and configuration

Here is a rough overview:

  1. Install conda (mamba or miniconda is fine).
  2. Install snakemake with:
conda install -c conda-forge -c bioconda snakemake
  1. Download checkm2 database (via wget https://zenodo.org/api/files/fd3bc532-cd84-4907-b078-2e05a1e46803/checkm2_database.tar.gz)
  2. Download GTDB-Tk database (via wget https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz)
  3. Download the latest release from this repo and cd into it
  4. Edit the config/config.yaml to provide the paths to your results/logs directories, and the paths to the databases you downloaded, as well as any parameters you might want to change.
  5. Edit the config/sampleData.csv file with the specific details for each assembly you want to check. Depending on what you enter here, the pipeline will automatically adjust what will be done.

General configuration

To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file.

"Main" section

Here you should provide the paths to your intermediary/results/logs directories. The interim directory will contain larger intermediary files. The results directory will contain the final output of the pipeline. The logdirectory will be used to store the log files for each step. Here you should also write the name of your sample data file (see relevant section below).

"Tools" section

Here you should give the paths to the databases needed for some of the tools.

sampleData file setup

The setup of the samples is specified via comma-separated values files (.csv). You can use the config/sampleData.csvfile as a template.