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# JASS analysis pipeline
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## Overview
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We present here a nextflow pipeline to harmonize, impute and analyze jointly GWAS summary statistics.

The current pipeline integrate the following workflow:

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![workflow image](./doc/workflow.png)

## Quick Start - Run pipeline on test data

Install nextflow as explain here : https://www.nextflow.io/docs/latest/getstarted.html

Clone the current repository locally:

```
    git clone https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline.git
```

Place your Reference Panel into the /Ref_Panel subfolder

Download and extract reference panel for LD-score in the pipeline folder:
```
    wget https://data.broadinstitute.org/alkesgroup/LDSCORE/eur_w_ld_chr.tar.bz2
    tar -jxvf eur_w_ld_chr.tar.bz2
```
Once done you can launch the pipeline as:

```
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    nextflow run jass_pipeline.nf --ref_panel {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/Ref_panel --gwas_folder {ABSOLUTE_PATH_TO_PIPELINE_FOLDER}/test_data/ -with-report jass_report.html

```
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## Required Input
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The following Item are necessary to run JASS pipeline on real data
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1. --meta_data : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/))
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2. --gwas_folder : A path toward a folder containing the summary statistics to analyze
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3. --ref_panel :A folder containing a Reference Panel in the .bim, .bed, .fam format
4. --ld-folder : A path toward a folder containing LD matrices (that can be generated from the reference panel with the raiss package as described here : http://statistical-genetics.pages.pasteur.fr/raiss/#precomputation-of-ld-correlation)
5. --group If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line

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## Optional parameters
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* --output_folder : A path toward a folder to write pipeline results (inittable, worktable...). by default results will be publish in the workflow directory.
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##  Usage Example on HPC Cluster

If you are working with a HPC server (Slurm job scheduler), you can adapt the nextflow_sbatch.config file and launch the pipeline with a command like:

sbatch --mem-per-cpu 32G -p common,dedicated,ggs --qos=long --wrap "module load java/13.0.2;module load singularity/3.8.3;module load graphviz/2.42.3;./nextflow run imputation_only.nf  -with-report imput_report.html -with-timeline imput_timeline.html -c nextflow_sbatch.config -qs 300"
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## Using docker container

Stable versions of JASS tools are available as docker container:


- JASS preprocessing:
https://quay.io/repository/biocontainers/jass_preprocessing?tab=tags

- JASS containers:
https://quay.io/repository/biocontainers/jass?tab=tags
- RAISS containers:
https://quay.io/repository/biocontainers/raiss?tab=tags