Humann: How to Set up / Run on Paired Files

The Beiting Lab-specific version of the Humann workflow is currently saved on the server at: /rome/software/labHumann

If you are planning to run it on a different server or your own computer, use the following command to download our lab-specific version, as Rich has created a separate repo on GitHub: git clone https://github.com/rdemko2332/labHumann.git

  1. Once you have cloned the repo or moved into the labHumann directory, use the following commands to create your container for the run:

    2. sudo docker ps -a #Lists all currently running containers

    sudo docker build . -t pig_test #Rename with name of container to be used for your run, where this command builds your container with that name

    sudo docker run -it -d pig_test #Rename with name of container, where this creates a running container

  2. After building your Docker container, you will need to make a few edits to make it able to run with your files:

    3. Open your editor for the .config file in the labHumann folder

    Under params:

    Edit the inputPath param to your directory with fastq files

    As currently written, these will need to be paired files that are in .fastq.gz format with the following suffix: _R{1,2}_001.fastq.gz

    Edit the resultDir param to the directory where you want your outputs to be saved

    This will create a new folder, if the folder that you are pointing to is not already created

    Update the kneaddataCommand param with any decontamination you want to do:

    Add decontamination steps using the following format: -db /kneadddata_databases/pig replacing pig with the name of your directory containing .bt2 files, where the directory should be stored at /venice/reference_db/kneaddata

    Remove any decontamination elements from the kneaddataCommand param that are not needed, where you should remove the whole section as: -db /kneadddata_databases/pig

    Under process:

    Edit container to the name of your container as defined above when building it in step 1

  3. Run the workflow using the following command: sudo nextflow main.nf -c docker.config

    4. **Recommend using screen to run, as the workflow takes a fairly long time to finish

    If you need to stop the workflow partway through, add -resume to step 3 above to restart

    Note that the process restarts at last sample that has not been completed, but it will not start part way through a step