get_Sample_TSV Instructions

This pipeline is designed to process VCF files by combining them with gnomAD AF / popmax_AF information. Additionally, it incorporates data from the geneHancer DB, which can be accessed here.

To use this script, ensure that the following directory structure is in place:

/
├── get_sample_TSV.nf
├── get_sample_TSV.json
├── process-selector.config (optional)
├── headers/
│   ├── interval_ID.header
│   ├── geneHancer_AnnotSV_elements.header
│   ├── gnomAD.header
├── bin/
│   ├── mergeGnomAD.sh
│   ├── getGnomAD.sh
│   ├── merge_chrom.py
│   ├── getSamples.sh
│   └── clean_tsv.py
├── data-read_only-layers_data-GeneHancer_AnnotSV_elements_v5.15.txt

Before executing the script, make sure to fill in the parameter file get_sample_TSV.json with the following values:

• gnomADByRegionDir: Directory where the gnomAD data should be saved or looked up if it already exists.
• DBXCLI: Path to dbxcli for Dropbox uploads.
• uploadDir: The Dropbox directory for uploading.
• VENV: Path to the virtual environment containing Pandas and NumPy.
• MAX_REGIONS: The maximum number of regions per gnomAD call (e.g., 10000).
• REGION_SPLIT_SIZE: If regions exceed MAX_REGIONS, files will be split, each containing this number of regions (e.g., 6000).
• cur_regions: The default peak bed file.
• all_samples: The default file containing paths to sample CSVs (processed by the process_VCF pipeline), can also be defined in the command line.
• output_dir: The output directory of the process, can be defined in the command line.

Inputs:

• sample_file: File where each line contains the path to a processed VCF file.
• params-file: JSON file with parameter configurations.
• upload: Set to 'true' to upload to Dropbox.
• bed_file: Region file in BED format.

Outputs:

• gnomADByRegionDir/regionFile/gnomAD: Directory containing gnomAD files by region.
• gnomADByRegionDir/regionFile/gnomAD/${regionFile.simpleName}.report: Report of getting gnomAD data
• gnomADByRegionDir/regionFile/samples_raw: Raw TSV file for samples.
• gnomADByRegionDir/regionFile/${regionFile.simpleName}.${sampleFile.simpleName}.prq: Table with combined data.

To run the script, follow these steps:

1. Open a terminal window.

2. Navigate to the directory containing the get_sample_TSV.nf script.

3. Execute the following command:

~/nextflow run get_sample_TSV.nf --sample_file data/read_only/samples/processed/all_samples.txt  -params-file get_sample_TSV.json --upload true -c process-selector.config

Explanation of the command:

• ~/nextflow run get_sample_TSV.nf: Initiates the Nextflow process using the get_sample_TSV.nf script.
• --sample_file data/read_only/samples/processed/all_samples.txt: Specifies the input file containing paths to processed VCF files.
• -params-file pipeline_param.json: Specifies the parameter configuration JSON file.
• --upload true: Enables the option to upload results to Dropbox.
• -c process-selector.config: Optionally uses the process-selector.config file for configuration (if available).

Make sure you have the required files and directories in place before running the script.