From b9a0711e7639ab322764f010bfcf5ea4f25d1129 Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hjulienn@maestro-submit.maestro.pasteur.fr>
Date: Tue, 16 Nov 2021 12:24:11 +0100
Subject: [PATCH] updated readme
---
README.md | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/README.md b/README.md
index 4f10cc3..cbe17df 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
--
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