VCF File Analysis Pipeline

This pipeline processes new VCF files to assess and analyze them for suspicious variants.

Input

• inputDir: The directory containing VCF / VCF.bgz files. These files can be located in subfolders.
• pathFile (optional): A text file containing the path to each processed VCF file.
• outputDir (optional): The directory where the processed VCF files will be saved.
• upload: Specifies whether to upload the processed file to Dropbox.

(Note: Optional parameters can be defined in the pipeline JSON file.)

Pipeline Steps

1. BGZip Unzipped VCF Files: Unzips and BGZips VCF files that are not already compressed.
2. TBI VCF Without Index File: Generates index files (TBI) for VCF files without an existing index.
3. Version Check: Verifies whether the VCF is in the hg38 version. The pipeline will drop files that are not the correct version.
4. VCF Processing: Processes the VCF files for analysis.
5. Upload Processed VCF: Uploads the processed VCF files if the upload parameter is set to true.

Pipeline Configuration (JSON File)

• all_samples: A text file containing the path to each processed VCF file.
• processedOutputDir: The default directory where processed VCF files will be saved.
• processedSamplesUploadDir: Directory path for uploading processed VCF files to Dropbox.
• DBXCLI: Path to dbxcli for Dropbox uploads.

Running the Pipeline

~/nextflow run process_new_sample.nf --inputDir NEW/VCF/FILES/DIR -params-file process_new_sample.json --upload true -c process-selector.config

Replace NEW/VCF/FILES/DIR with the actual path to the directory containing your VCF files. Adjust other parameters and options as needed.