TL;DR

If you want to run YAMP:

1. Install Nextflow, Docker and/or Singularity, as explained here.

2. From the command line clone the YAMP GitHub repository, which includes several configuration files (described here):

   git clone https://github.com/alesssia/YAMP.git
   

3. Enter the YAMP folder:

   cd YAMP
   

4. Download the additional resources, as explained here.

5. Run YAMP (with paired-end reads, default parameters, using docker containers):

   nextflow run YAMP.nf --reads1 myfile_R1.fq.gz --reads2 myfile_R2.fq.gz --prefix name 
      --mode complete -profile base,docker
   

   Do you have single-end reads? No problem, run:

   nextflow run YAMP.nf --reads1 myfile_R1.fq.gz --singleEnd true --prefix name
     --mode complete -profile base,docker
   

Do you want to know more? Have a look at the other tutorials in this wiki!