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How to run metaGOflow

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Haris Zafeiropoulos edited this page Oct 26, 2022 · 17 revisions

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 -e ERR855786 -d output_folder -n ERR855786 -s

Using an ENA accession id

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

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:

Anything unclear or inaccurate? Please open an issue or email Dr.Haris Zafeiropoulos ([email protected]).

With respect to EMO BON protocols, samples, analyses you may contact the Observation, Data and Service Development Officer of EMBRC, Dr. Ioulia Santi ([email protected])

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