NextFlow_RD_Genomic

Tasks

• Create the directory data/qsr_vcfs
• Populate with https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
• Populate with https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx
• Make the modules/BSQR.nf module
• Search main.nf for changes (note the channel creation and usage)
• Update the nextflow.config

Description

A simple base Rare disease and germline genomics pipeline to test the effects of down-sampling on variant calling

Basic Overview

Using the NextFlow workflow software to run the following pipeline

Pipeline

Index genome > Fastqc analysis > Align reads > Downsample bam files > Sort bam > Mark duplicates > Index bam > Call variants > Hard filter

Setup

To run the pipeline, we need to obtain

• A genome build (GRCh38) - provided by the Broad institute

$ cd data/genome
$ wget https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta

• FastQ sample (for workflow development)

$ cd ../samples
$ wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR151/003/SRR1518253/SRR1518253_1.fastq.gz && \
wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR151/003/SRR1518253/SRR1518253_2.fastq.gz && \
gunzip *.gz

• When scaling up, FastQ samples

$ wget https://genomics.viapath.co.uk/benchmark/files/FASTQ/NA12878_WES.zip

$ wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz &&
wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz &&
wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/hapmap_3.3.hg38.vcf.gz &&
wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/1000G_omni2.5.hg38.vcf.gz &&
wget https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx &&
wget https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi &&
wget https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi &&
wget https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi

Running the pipeline

# Using Docker
$ nextflow run -profile docker main.nf

# Using docker in singularity
$ nextflow run -profile singularity main.nf

Validating the pipeline

See https://genomics.viapath.co.uk/benchmark

DNANexus applet setup (A local applet for basic testing)

• DNANexus Python Bindings Documentation
• Install the app

pip install -r requirements.txt

• Routine maintenance Periodically update dxpy

$ pip install --upgrade dxpy

DNANexus Tutorial

• Overview videos
• Developer tutorial

$ dx select <your-project-name>
$ dx build --nextflow