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N-Hoffmann merged 1 commit into from
May 20, 2025
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Update README #41

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Expand Up @@ -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
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