single_config.md

Prepare config files for single samples

MoTrPAC human samples must be run as singletons.

A configuration (config) file is a file in JSON format that specifies input parameters required to run the ATAC-seq pipeline. Find comprehensive documentation of definable parameters here.

This tutorial walks you through the steps to quickly generate config files for a large number of samples with the same runtime parameters (e.g. memory requirements, reference genome).

You will need to define a few paths first:

1. base_json: A trucated JSON file with paramaters that are constant for all samples in this batch. Find an example here. /path/to/genome.tsv refers to the path to either "motrpac_rn6.tsv" or "motrpac_hg38.tsv" file generated in Step 3. Note that you must include the following parameters for consistency within MoTrPAC:

    "atac.genome_tsv" : "/path/to/genome.tsv",
    "atac.paired_end" : true,
    "atac.multimapping" : 4,
    "atac.auto_detect_adapter" : true,
    "atac.enable_idr" : true,
    "atac.paired_end" : true,

2. fastq_dir: The path to the FASTQ files for all samples in this batch. Note that FASTQ files should be named by vial label, e.g. 90013015505_R1.fastq.gz.
3. config_dir: The path to the desired output directory for the generated config files.

After you have defined the full paths in the variables described above, run the following command:

$ bash src/make_json_singleton.sh ${base_json} ${fastq_dir} ${config_dir} 

The result will be a single JSON-formatted config file in ${config_dir} for each sample included in ${fastq_dir}. Click here to see an example of what these config files should look like.