diff --git a/README.md b/README.md index 4f10cc337a0266cb2b2ff860165a271adb36a301..cbe17df75b9110e8cdcce641c18de56fd84813b2 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,7 @@ Download and extract reference panel for LD-score in the pipeline folder: Once done you can launch the pipeline as: ``` + 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 ``` @@ -51,3 +52,16 @@ The following Item are necessary to run JASS pipeline on real data 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" + +## 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