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Getting Started

Install necessary dependencies​

warning

To successfully run the gwas-sumstats-harmoniser, it is crucial to have the following dependencies installed:

  • Linux or macOS
  • HTSlib for tabix
  • Nextflow
  • Docker, Singularity, or Anaconda
  1. Install HTSlib
wget https://github.com/samtools/htslib/releases/download/1.21/htslib-1.21.tar.bz2
cd htslib-1.21
./configure --prefix=/where/to/install
make
make install
export PATH=/where/to/install/bin:$PATH
  • Confirm the htslib installation by
$ tabix

Version: 1.9
Usage:   tabix [OPTIONS] [FILE] [REGION [...]]
  1. Install Nextflow
java -version # Java v8+ required
# openjdk 11.0.13 2021-10-19
curl -fsSL get.nextflow.io | bash
chmod +x nextflow
mv nextflow ~/bin/
  • Confirm the the nextflow installation by
$ nextflow info

Version: 24.10.0 build 5928
Created: 27-10-2024 18:36 UTC (18:36 BST)
System: Linux 4.18.0-513.5.1.el8_9.x86_64
Runtime: Groovy 4.0.23 on Java HotSpot(TM) 64-Bit Server VM 17.0.4.1+1-LTS-2 Encoding: UTF-8 (UTF-8)
  1. Next, install Singularity, Docker or Anaconda. Note that using Singularity or Docker is recommended.
  • Before starting the installation, it's a good idea to check if any of these tools are already installed on your system:
$ singularity --version
singularity-ce version 4.1.4-1.el8

$ docker --version
Docker version 27.2.0, build 3ab4256

$ conda --version
conda 23.11.0

Run your first harmonisation pipeline​

To run your first harmonization pipeline, execute the following command:

nextflow run  EBISPOT/gwas-sumstats-harmoniser -r $release_version -profile test,singularity

🚨 If you did not choose to install Singularity, remember to replace singularity with docker or conda.

Once Nextflow starts running:

  1. It will download the gwas-sumstats-harmoniser pipeline from Github into the global cache ~/.nextflow/assets. (Please note that in the nextflow, -r determines which version of the pipeline to use, for example, "v1.1.10"; while --version will only decide what is recorded in the running.log file.)
  2. It will pull the Docker image from Docker Hub and built Singularity container.
  3. Using the input files random_name.tsv,random_name.tsv-meta.yaml along with a small test reference file provided in the ~/.nextflow/assets/EBISPOT/gwas-sumstats-harmoniser/test_data, it will execute the pipeline.
  4. Once the pipeline executes, you can monitor the progress in the terminal, which may look like this:
 N E X T F L O W   ~  version 24.04.2

Launching `https://github.com/EBISPOT/gwas-sumstats-harmoniser` [maniac_mestorf] DSL2 - revision: 67198bb9e7

Harmonizing the file ~/.nextflow/assets/EBISPOT/gwas-sumstats-harmoniser/test_data/random_name.tsv
executor >  local (13)
[9a/05e067] NFC…ATALOGHARM:major_direction:map_to_build (random_name) | 1 of 1 ✔
[cc/fef59c] NFC…ajor_direction:ten_percent_counts (random_name_chr22) | 2 of 2 ✔
[46/626f6f] NFC…:major_direction:ten_percent_counts_sum (random_name) | 1 of 1 ✔
[1c/b92ff2] NFC…_direction:generate_strand_counts (random_name_chr22) | 2 of 2 ✔
[b7/3f81cb] NFC…major_direction:summarise_strand_counts (random_name) | 1 of 1 ✔
[67/216e41] NFC…TALOGHARM:main_harm:harmonization (random_name_chr22) | 2 of 2 ✔
[a9/336d51] NFC…OGHARM:main_harm:concatenate_chr_splits (random_name) | 1 of 1 ✔
[64/8a8fec] NFC…HARM:GWASCATALOGHARM:quality_control:qc (random_name) | 1 of 1 ✔
[6e/fb619c] NFC…GHARM:quality_control:harmonization_log (random_name) | 1 of 1 ✔
[48/1ae6d4] NFC…OGHARM:quality_control:update_meta_yaml (random_name) | 1 of 1 ✔
[chr1, chr22,  is being harmonized]

In your current directory, you will find a folder named random_name that contains all intermediate files and the final result.

./random_name/
├── 1_map_to_build
│   ├── 1.merged
│   ├── 22.merged
│   ├── random_name.tsv-meta.yaml
│   └── unmapped
├── 2_ten_sc
│   ├── ten_percent_chr1.sc
│   └── ten_percent_chr22.sc
├── 4_harmonization
│   ├── chr1.merged.hm
│   ├── chr1.merged.log.tsv.gz
│   ├── chr22.merged.hm
│   └── chr22.merged.log.tsv.gz
├── 5_qc
│   ├── harmonised.qc.tsv
│   ├── harmonised.tsv
│   └── report.txt
├── final
│   ├── random_name.h.tsv.gz
│   ├── random_name.h.tsv.gz-meta.yaml
│   ├── random_name.h.tsv.gz.tbi
│   └── random_name.running.log
└── ten_percent_total_strand_count.tsv

This output confirms that the pipeline has been successfully executed and is ready to process larger real datasets.