hivlab / ena-upload

Snakemake workflow to upload Sars-Cov-2 reads to ENA

ena-upload

Snakemake workflow to trim and upload Sars-Cov-2 reads to ENA. This workflow uses ena-upload-cli for upload and updated process_xlsx.py script for metadata table preparation from Galaxys ena_upload tool. Raw reads are adapter-trimmed using bbduk.sh tool and mapped to host/human reference genome using bbmap.sh.

Install

• Download and install miniconda3: https://docs.conda.io/en/latest/miniconda.html.
• Clone this repo and create conda environment

git clone https://github.com/avilab/ena-upload.git
cd ena-upload
conda env create -f workflow/envs/environment.yml

Running

Update files in config directory:

• metadata.csv sample metadata (sample_name, collection_date, experiment id, runs/raw read file names)

• pep.yaml peppy configuration file to provide full paths to raw reads.

• config.yaml study wide configuration.

• Check upload rule flags in Snakefile, by default, TEST submission (--dev flag in extra parameter) with 'add' action is performed.

• Create .secret.yml file with Webin credentials.

• Activate conda environment.

conda activate ena_upload

• Test run:

snakemake -n --use-conda

• Run:

snakemake -j --use-conda

• Hold your breath.

Workflow graph

snakemake --dag -d .tests/ | dot -Tsvg > resources/rulegraph.svg