Nextflow Configuration

This README documents the parameters used in the nextflow configuration file. Some default values for configuration variables are initially set up to facilitate the demonstration test-run.

Parameter	Description
large_files	Directory containing large external resources (e.g. gnomAD, MANE, AlphaMissense). See large_files README for instructions on how to source this content
processed_annotations	Output directory for all processed/reformatted data. Cohort/callset independent, to be used across multiple runs.
outputDir	Defaults to processed_annotations, required for the 'workflow outputs' NextFlow functionality. Override for Annotation/Talos workflow using -output-dir <path>
input_vcf_extension	Linked to shards. If a sharded VCF is provided, this argument is the file extension to glob for. By default this is vcf.bgz, but could be altered to vcf.gz.
alphamissense_tsv	Path in large_files to the AlphaMissense raw data, reformatted to be used in Hail annotation
alphamissense_zip	Path in processed_annotations to the reformatted AlphaMissense data, ready to be used by Echtvar for annotation
ensembl_bed	Path in processed_annotations to the Ensembl BED file, one line per gene
ensembl_merged_bed	Path in processed_annotations to the Ensembl BED file, overlapping regions merged
mane_json	Path in processed_annotations to pre-processed MANE data
mitimpact_zip	Path in processed_annotations to the reformatted MitImpact reference data
mitotip_zip	Path in processed_annotations to the reformatted MitoTip reference data
napogee_zip	Path in processed_annotations to the reformatted nAPOGEE reference data
ensembl_gff	Path in large_files to the Ensembl GFF3 file
gnomad_zip	Path in large_files to the echtvar annotation file from Zenodo
mane	Path in large_files to the MANE transcript data
ref_genome	Path in large_files to the reference genome FASTA file
hpo	Path in large_files to the HPO ontology file in .obo form
gen2phen	Path in large_files to the Geno~Phenotype databset in .txt form
phenio_db	Path in large_files to the Monarch Phenotype DB in .db.gz form
mitimpact_tsv	Path in large_files to the raw Mitimpact file
mitotip_tsv	Path in large_files to the raw MitoTip file
napogee_tsv	Path in large_files to the raw Mitochondrial nAPOGEE file
submission_summary	FTP URL for weekly ClinVar submission dump
variant_summary	FTP URL for weekly ClinVar variant dump
clinvar_blacklist	A string, containing quoted, space-delimited entries for all ClinVar submitter sites to blacklist (ignore).
container	Docker image to use
docker.enabled	Parameter for Nextflow to enable usage of Docker