olopade-lab / alignment

This is the WGS alignment workflow corresponding to the manuscript Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes (Ansari-Pour and Zheng, et al; under review). It is based on the GATK4 format conversion and best-practices workflows.

Installation

First, checkout this repository:

git clone --recurse-submodules https://github.com/olopade-lab/alignment.git

A unix-based operating system, Docker, and Java 8 is required. To download the version of cromwell corresponding to the manuscript above, run

bash scripts/download_cromwell.sh

To download the most recent cromwell release, visit the cromwell releases page. It is recommended to run with Singularity. To run the helper script to make input lists, Python 3 is required.

Configuration

The Cromwell configuration can be found here. The workflow configuration can be found here. There is an example config with small truncated input files for testing here. The configuration should specify the location of the raw input data in TSV format. Example files are included. Both fastq and bam inputs are supported.

If using the Singularity configuration, all required images will be downloaded once and cached. The location of the cache can be configured by setting the environment variable SINGULARITY_CACHEDIR (default is $HOME/.singularity/cache).

The workflow configuration is based on the GATK recommendation for b37, found here. We are using the human_g1k_v37 reference, which is identical to b37 except that it is missing some decoy sequences. See here and here for more details.

Execution

To run the small example (this should work out-of-the-box-- just substitute your cromwell executable name below):

java -jar cromwell-55.jar run align.wdl -i configs/small_test.HumanG1Kv37.json

To run the full workflow on Dolores using Singularity:

java -Dconfig.file=configs/singularity_slurm.conf -jar cromwell-55.jar run align.wdl -i configs/HumanG1Kv37.json

Note this must be run from a machine with Singularity available (any of the compute nodes.) A helper script for creating the input file TSV lists can be found here.