EOSC pilot project

Requirements

• Java 8 (or later)
• Docker 1.10 (or later)
• GATK 3.7

Note: This workflow is provided with a Docker with including all required dependencies except GATK which cannot be distributed due to license restrictions.

Quickstart

1. Download the GenomeAnalysisTK.jar (version 3.7) package from this link, untar and save it in a path in your computer.

2. Install Nextflow with the following command:

    curl -s https://get.nextflow.io | bash 
   

note: you can also install it as a Conda package:

    conda install nextflow -c bioconda

3. Launch a execution with test data use following command:

    nextflow run CRG-CNAG/EOSC-Pilot --gatk </full/path/to/GenomeAnalysisTK.jar>
   

Pipeline parameters

--genref

Specify the reference genome. Can be either: test,v37 or v38.

For example:

    nextflow run CRG-CNAG/EOSC-Pilot --genref v38

--index

The dataset index file. A tab separated file formatted as shown below:

sample_alias	file_stable_id	archive_ebi_fullpath
gonl-16a	EGAF00000513247	data/test2/fastq/101231_I305_FC810N3ABXX_L7_HUMrutRGVDIAAPE_1.fq.gz
gonl-16a	EGAF00000513248	data/test2/fastq/101231_I305_FC810N3ABXX_L7_HUMrutRGVDIAAPE_2.fq.gz
gonl-16a	EGAF00000513249	data/test2/fastq/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz
gonl-16a	EGAF00000513250	data/test2/fastq/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz
gonl-16a	EGAF00000513251	data/test2/fastq/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz

--intervals

The intervals bed file.

Execution DAG

Components

This project users the following software packages or libraries

• R
• Pcard 2.9
• bwa 0.7.15
• fastqc 0.11.5
• sambamba 0.6.6
• Tabix
• GATK 3.7