Singularity (v. 3) and NextFlow (>= v. 20.10.0). Containers with the software for each step are pulled from the Sylabs cloud library (https://cloud.sylabs.io/library).
Paths to various generic files (e.g., bwa indices) must be included in the nextflow.config file -- check that file and change paths accordingly. These include:
- Blacklist bed files for each genome
- Chrom size files for each genome
- BWA indices
- TSS files (BED6 files denoting TSS positions)
You'll also need to set the params.results variable -- either in the nextflow.config file itself, or on the command line when you run the pipeline ('--results /path/to/results').
Lastly, you'll need to include information about each ATAC-seq library, including the genome that each library should be mapped to and the paths to the fastq files for each readgroup. Organize this information in a JSON file, as in library-config.json.
Once you have all of the above information, you can run the pipeline as follows (in this case, indicating the path to the results on the command line):
nextflow run -params-file library-config.json --results /path/to/results /path/to/main.nf