pandora_paper_roc

A snakemake pipeline that receives as input variant calls from several tools and build several data and plots for the pandora paper, the main one being the ROC plot. See the pandora paper for more details.

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:

unzip sample_data.zip (TODO: add link)
source venv/bin/activate
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 locally:

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

If you want to run just on illumina or nanopore data

Use the config.pandora_paper_tag1.illumina.yaml or the config.pandora_paper_tag1.nanopore.yaml config files.

Exploring pandora filters

Config files config.pandora_paper_tag1.illumina.filters.yaml and config.pandora_paper_tag1.nanopore.filters.yaml contain the configuration to explore how filters change pandora and other tools results.

Exploring the effect of methylation-aware guppy basecalling

Config files config.pandora_paper_tag1.4_way_new_basecall.yaml and config.pandora_paper_tag1.4_way_old_basecall.yaml contain the configuration to run pandora with new (methylation-aware guppy) and old (normal guppy) basecalled ONT reads.

Troubleshooting

If you get an error similar to this (this is an example):

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/.