From 9a9af750cd86ecfd3f430882befaefbb7843471c Mon Sep 17 00:00:00 2001 From: N-Hoffmann Date: Tue, 20 May 2025 15:15:30 +0200 Subject: [PATCH] Update README System requirements and usage with Singularity --- README.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/README.md b/README.md index 55e7171..857a62a 100755 --- a/README.md +++ b/README.md @@ -23,12 +23,24 @@ ANNEXA works by using only three parameter files (a reference genome, a referenc This pipeline has been tested with reference annotation from Ensembl and NCBI-RefSeq. +## System requirements +ANNEXA requires 0.5GB of disk space for installation, and requires at least 16 GB of RAM and 2 CPU threads to run the test example. +By default, it requires. 40 GB of RAM and 8 CPU threads. This can be changed in the options (see Performance options). + ## Usage 1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) +(Optional) If you are using Linux, we recommend installing [Apptainer](https://apptainer.org/docs/user/main/quick_start.html) (formerly Singularity) to handle tools used by ANNEXA. 2. Test the pipeline on a small dataset +```sh +nextflow run IGDRion/ANNEXA \ + -profile test +``` + +Or, if you have installed Apptainer: + ```sh nextflow run IGDRion/ANNEXA \ -profile test,singularity