garyluu/wdl-pcawg-bwa-mem-workflow

WDL implementation of https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow

ICGC-TCGA-PanCancer BWA Workflow

Overview

This is the workflow for the TCGA/ICGC PanCancer Analysis of Whole Genomes (PCAWG) project that aligns whole genome sequences with BWA-Mem.

For more information about the project overall see the PanCancer wiki space.

More detailed documentation about the production use of this workflow can be found in the PanCancer-Info project where we maintain our production documentation and SOPs.

Building the Worklfow Docker Image

You can also build a Docker image that has the workflow ready to run in it.

docker build -t pcawg-bwa-mem-workflow

Running the Workflow with Cromwell

java -jar cromwell-19.3.jar run pcawg-bwa-mem-workflow.wdl pcawg-bwa-mem-workflow.json

Sample Data

Some synthetic sample data.

• https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal2.bam
• https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/synthetic_bam_for_GNOS_upload/hg19.chr22.5x.normal.bam

Reference Data

We use a specific reference based on GRCh37.

• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.fai
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.amb
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.ann
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.bwt
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.pac
• http://s3.amazonaws.com/pan-cancer-data/pan-cancer-reference/genome.fa.gz.64.sa

Authors

• Brian O'Connor [email protected]
• Junjun Zhang [email protected]
• Adam Wright [email protected]

Contributors

• Keiran Raine: PCAP-Core and BWA-Mem workflow design
• Roshaan Tahir: Original BWA-Align workflow design
• Adam Struck: WDL implementation