IGV-snapshot-nf

An example Nextflow workflow for creating automated IGV snapshots of .bam files based on a list of target regions.

This workflow is designed to show how to integrate automated IGV snapshotting into a Nextflow workflow.

Installation

First, clone this repository:

git clone https://github.com/stevekm/IGV-snapshot-automator.git
cd IGV-snapshot-automator

Containers

Docker and/or Singularity containers are used to package IGV, X11, and xvfb required for functionality. Docker is required to build Singularity containers

To build the Docker container for IGV:

cd containers
make docker-build VAR=IGV

To test out the IGV Docker container:

make docker-test VAR=IGV

(optional) To build a Singuarity container for IGV, first build the Singularity Docker container:

make docker-build VAR=Singularity-2.4

• This container is used to build Singularity containers

To build the Singularity container for IGV:

make singularity-build VAR=IGV

# test the container:
make singularity-test VAR=IGV

• The Singularity container will be saved to containers/IGV/IGV.simg, which you can upload to your remote server for usage

Usage

Run the included demo workflow (from the parent repo directory):

make run

Should look something like this:

IGV-snapshot-nf$ make run
./nextflow run main.nf -profile "docker"
N E X T F L O W  ~  version 19.04.1
Launching `main.nf` [kickass_cray] - revision: 1823b32e4f
~~~~~~~ IGV Pipeline ~~~~~~~
* Project dir:        /Users/steve/projects/IGV-snapshot-nf
* Launch dir:         /Users/steve/projects/IGV-snapshot-nf
* Work dir:           /Users/steve/projects/IGV-snapshot-nf/work
* Profile:            docker
* Script name:        main.nf
* Script ID:          1823b32e4f4fbc1caa63b0c12b2d4340
* Container engine:   docker
* Workflow session:   843f9541-9cc2-46c8-9005-89659c67ed80
* Nextflow run name:  kickass_cray
* Nextflow version:   19.04.1, build 5072 (03-05-2019 12:29 UTC)
* Launch command:
nextflow run main.nf -profile docker
[warm up] executor > local
executor >  local (1)
[91/852794] process > run_IGV [100%] 1 of 1 ✔
Completed at: 22-May-2019 15:27:46
Duration    : 1m 20s
CPU hours   : (a few seconds)
Succeeded   : 1

Example snapshot output:

Software

• Tested with macOS 10.12.6 and RHEL 7

• Nextflow (requires Java 8+ and bash)

• IGV 2.4.10

• Python