AIAP Test Version

Usage

0. Install Nextflow

Refer to the Nextflow documentation for installation instructions.

1. Build the Singularity Image

First, build the singularity image using the provided definition file:

singularity build --fakeroot aiap-nf.sif aiap-nf.def

Alternatively, you can use any other singularity image that contains the required tools.

2. Prepare Input Files

• Sample Sheet: Edit samplesheet-demo.csv (filename can be changed) to include your samples.
• Configuration: Edit params-demo.json (filename can be changed) to specify your pipeline parameters.

3. Run the Pipeline

You can run the pipeline using:

nextflow run tyfu-cc/aiap -params-file /path/to/params/json/file -with-singularity /path/to/your/sif/file

Or, if you've cloned the pipeline locally, navigate to its directory and run:

nextflow run main.nf -params-file /path/to/your/params/json/file -with-singularity /path/to/your/sif/file