ICGC ARGO DNA Seq Processing Pipeline

Introduction

This repository maintains the source code of the ICGC ARGO DNA Seq Processing Pipeline. The pipeline is written in Nextflow workflow language using DSLv2, with modules imported from other ICGC ARGO GitHub repositories. Specifically, here are repositories maintaining various of tools/modules:

• https://github.com/icgc-argo/dna-seq-processing-tools
• https://github.com/icgc-argo/data-processing-utility-tools
• https://github.com/icgc-argo/nextflow-dna-seq-processing-tools
• and https://github.com/icgc-argo/data-qc-tools-and-wfs

Each Nextflow module (including associated container image which is registered in Quay.io) is strictly version controlled and released independently. To ensure reproducibility the pipeline declares explicitly which specific version of a module is to be imported.

Major tasks performed in the pipeline

• download input sequencing metadata/data from SONG/SCORE
• preprocess input sequencing reads (in FASTQ or BAM) into lane level (aka read group level) BAM
• collect CollectQualityYieldMetrics using Picard tool for read group
• perform BWA-MEM alignment against GRCh38 reference genome in parallel for each lane BAM
• merge and markduplicate aligned lane BAM, produce coordinate-sorted CRAM/CRAI and duplicates_metrics
• collect alignment QC metrics using samtools stats for aligned seq
• collect CollectOxoGMetrics using GATK for aligned seq and calculate OxoQ score
• generate SONG metadata for aligned seq and upload them to SONG/SCORE
• generate SONG metadata for all collected qc_metrics and upload them to SONG/SCORE

Run the pipeline

To run the pipeline, please follow instruction here to install Nextflow (version 20.01.0 or higher) first.

Run 1.3.0 version of the pipeline:

nextflow run icgc-argo/dna-seq-processing-wfs -r 1.3.0 -params-file <your_params_file.json>

You may need to run nextflow pull icgc-argo/dna-seq-processing-wfs if the version 1.3.0 is new since last time the pipeline was run.

Please note that SONG/SCORE services need to be available and you have appropriate API token.

Testing

Automated Travis CI testing has been set up. However, tests relying on SONG/SCORE will be skipped when CI is triggered on a Travis server where SONG/SCORE services are not available. When running tests locally (where SONG/SCORE services may be available) please use the following commands under the root directory of this Git repository:

# perform all tests when SONG/SCORE is available
export api_token=<your_api_token>
pytest -v

# or perform tests that do not need SONG/SCORE
TRAVIS=true pytest -v