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> |
outdir |
Used to create an output path for all cohort-specific outputs, resulting folder is {params.outdir}/{cohort}_outputs |
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 |
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 |
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 |