Pandora workflow

Snakemake pipeline to run pandora with and without denovo enabled.

The version used in the pandora paper review has tag pandora_paper_update_31_03_2021.

The version used in the pandora paper submission has tag pandora_paper_tag1.

Running

Requirements

Dependencies

• python 3.6+;
• singularity 2.4.1+;

Setting up virtualenv

./setup.sh

Running on the sample example:

1. Download sample data (TODO: add link);
2. unzip sample_data.zip
3. source venv/bin/activate
4. bash scripts/run_pipeline_local.sh -j8

Running on the paper data:

1. git checkout pandora_paper_tag1
2. source venv/bin/activate

If you want to run local:

3. bash scripts/run_pipeline_local.sh -j <NB_OF_THREADS> --configfile config.pandora_paper_tag1.yaml

If you want to run on an LSF cluster:

3. bash scripts/submit_lsf.sh --configfile config.pandora_paper_tag1.yaml

Troubleshooting

If you get this error:

Building DAG of jobs...
Pulling singularity image docker://leandroishilima/subsampler:pandora_paper_tag1.
WorkflowError:
Failed to pull singularity image from docker://leandroishilima/subsampler:pandora_paper_tag1:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR: Image file exists, not overwriting.

  File "/hps/nobackup2/iqbal/leandro/pandora_paper_tag1/subsampler/venv/lib/python3.7/site-packages/snakemake/deployment/singularity.py", line 88, in pull

pass to the running script the default location where singularity images are store. For example, in the EBI cluster, it would be --singularity-prefix /nfs/leia/singularity/leandro/.