Active development

Are you sad that your favorite binner didn't make it into the metaGEM workflow? Have you developed a new bioinformatics tool that you would like to see incorporated into metaGEM? Want alternative tools for certain tasks or even new additional features? We want to hear from you!

If you want to see any new additional or alternative tools incorporated into the metaGEM workflow please do not hesitate to raise an issue or create a pull request. Snakemake allows workflows to be very flexible, and adding new rules is as easy as filling out the following template and adding it to the Snakefile:

rule package-name:
    input:
        rules.rulename.output
    output:
        f'{config["path"]["root"]}/{config["folder"]["X"]}/{{IDs}}/output.file'
    message:
        """
        Helpful and descriptive message detailing goal of this rule/package.
        """
    shell:
        """
        # Well documented command line instructions go here
        
        # Load conda environment 
        set +u;source activate {config[envs][package]};set -u;

        # Run tool
        package-name -i {input} -o {output}
        """

Please note that you will not be able to use the metaGEM.sh parser to submit jobs for any rules that you create for yourself without adapting the parser first. You will have to manually submit jobs to the cluster or add this rule to the metaGEM.sh parser yourself. You are more than welcome to ask us for help doing this.