Chicxulub

A Nextflow pipeline for computationally intensive searches of large-scale bottom-up proteomics datasets.

Usage

1. Ensure that you are on a system that has Apptainer, Nextflow, and SLURM.
2. Clone the repositiory by running git clone https://github.com/stavis1/chicxulub
3. Edit the nextflow.config file where indicated to use your SLRUM account, maximum queue size, desired partition, and quality of service.
4. Make edit the default_params.txt file for your experiment and place it in the same folder as your .mzML and .fasta files.
5. Fill out a design.tsv file based on the template. All paths in the file should be absolute.
6. Run nextflow run /path/to/proteomics_cluster_submission/main.nf --design design.tsv