This pipeline processes new VCF files to assess and analyze them for suspicious variants.
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.)
- BGZip Unzipped VCF Files: Unzips and BGZips VCF files that are not already compressed.
- TBI VCF Without Index File: Generates index files (TBI) for VCF files without an existing index.
- Version Check: Verifies whether the VCF is in the hg38 version. The pipeline will drop files that are not the correct version.
- VCF Processing: Processes the VCF files for analysis.
- Upload Processed VCF: Uploads the processed VCF files if the
upload
parameter is set to true.
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.
~/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.