How to run metaGOflow

To demonstrate how one may run the metaGOflow workflow, we will use a marine Illumina MiSeq shotgun metagenome with the ENA accession run id ERR855786.

Using local raw data files

./run_wf.sh -f SRR1620013_1.fastq.gz -r SRR1620013_2.fastq.gz -n prefix_for_output_files -d output_folder_name

Using an ENA accession id

In this case, the user may need to run either public or private data. For the first case, things are quite straight forward:

./run_wf.sh -e ERR855786 -d output_folder -n ERR855786 -s

In case of private data,

The config.yml file

Run in HPC

Docker or Singularity

metaGOflow may run using Docker (default) or Singularity container technology. To enable Singularity, you may add the -s argument when calling metaGOflow. In addition, there is a case where Singularity images need to be force-pulled. In this case, you need to run the get_singularity_images.sh.

cd Installation
bash get_singularity_images.sh

Thus, to run metaGOflow using Singularity, run: