Given an 'Undetermined' fastq file (or several undetermined fastq files), this program tells the user how many barcodes of each type were present in each file.

Install conda (if you don't already have it, or if you'd like a better conda) with: https://github.com/conda-forge/miniforge#mambaforge

This link will install a version of conda called 'mamba' that also includes conda. mamba runs faster than conda, results in fewer ambiguities when resolving packages, and is easier to install on a per-user basis. For best results with this pipeline, use mamba. Don't forget to read the instructions at the end of the setup script regarding logging out and back in.

Install snakemake in an environment called snakemake with:

mamba create -c conda-forge -c bioconda -n snakemake snakemake

or (if you didn't install mamba) with:

conda create -c conda-forge -c bioconda -n snakemake snakemake

• Download the contents of this git repo to a folder on your machine and cd into that folder (so that "ls" shows count_undetermined_barcodes.smk).
• Open the count_undetermined_barcodes.yaml file and fill in the variables using instructions from the comments
• Activate snakemake with:

mamba activate snakemake

• Run the first step with:

snakemake -s count_undetermined_barcodes.smk --cores 10

In the future, if a user provides sample sheet and barcode labeling file, this program also will tell the user what barcodes and what samples the undetermined barcodes might map to.