Test Run

To test the the workflow, we recommend the following steps:

Install Dependencies

Miniconda is used to create software environments necessary to run the workflow. The workflow is then run using the workflow engine Snakemake. In order to run the workflow with Singularity, a working Singularity 3.5 installation is needed. For details installing these dependencies, see Install Dependencies.

Download the workflow

$ git clone https://gitlab.com/schmeierlab/workflows/metafunc.git && cd metafunc

Create a mapping reference index of the host (here human)

# download host genome
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh38.primary_assembly.genome.fa.gz
gzip -d GRCh38.primary_assembly.genome.fa.gz

# download corresponding gene annotation
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.primary_assembly.annotation.gtf.gz
gzip -d gencode.v33.primary_assembly.annotation.gtf.gz

# build STAR index
conda create --yes -n star star=2.7.3a
conda activate star
mkdir genome
STAR --runMode genomeGenerate --runThreadN 12 --genomeDir genome --genomeFastaFiles GRCh38.primary_assembly.genome.fa

Download provided Kaiju Database

wget https://zenodo.org/record/5602178/files/kaijudb_nreuk_202001.tar.bz2
tar xvjf kaijudb_nreuk_202001.tar.bz2 && rm kaijudb_nreuk_202001.tar.bz2

Download provided nr-go database for nr_euk:

wget https://zenodo.org/record/5602157/files/nrgo_202001_updated.tar.bz2
tar xvjf nrgo_202001_updated.tar.bz2 && rm nrgo_202001_updated.tar.bz2

Run the workflow

The config-file is setup to work with the test-data in a .test directory within the workflow, using only Viruses for microbiome functional output. Run the workflow either in conda-only or singularity-only mode:

# conda-mode
snakemake -p --use-conda --cores 12 --resources const=1 --configfile config.yaml > run.log 2>&1

# singularity-mode
snakemake -p --use-singularity --cores 12 --resources const=1 --configfile config.yaml > run.log 2>&1