AVT parameters

These values are over-written by command line arguments passed to nextflow run in the submission script submit.sh.

For a complete list of workflow parameters (configurable parameters have a params. prefix), you can run:

nextflow config -flat -profile <profile_name> main.nf | grep ^params

All parameters have a default value, which is listed here. To change the parameter, add it to your submission script.

Category	Parameter	Notes	Default
General parameters	--outdir	The location of the output files	.
	--publish_all	whether to publish the intermediate files	false
Input	--region_input_file	file that specifies the region of the genome that needs to be processed	"${projectDir}/input/chromosomes_subset.txt"
	--exclusion_data_file	a text file containing genomic regions to be excluded	false
	--input_cohort_file	case/control cohort	"/gel_data_resources/workflows/input_material/RDP_tools_aggregateVariantTestingWorkflow/auxiliary_files/input/cohort.txt"
	--cohort_sample_column	The column in your cohort file that specifies the platekey	"Platekey"
	--cohort_sex_column	The column in your cohort file that specifies the sex	"sex"
	--control_coding	How controls are coded in your input file	0
	--phenotype_array	List of columns in your input file that contain phenotype data	"status"
	--phenotype_type_array	List of phenotype types that correspond to the list of phenotype columns	"b"
	--covariates	List of columns of covariates in your input file (for SAIGE-GENE and REGENIE branches) - please use false if no covariates are needed for SAIGE-GENE and REGENIE. This parameter does not affect the Fisher's test branch at all	"age,sex,age.age,age.sex,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20"
	--categorical_covariates	List of columns of discrete covariates in your input file (for SAIGE-GENE and REGENIE branches) - please use false if no categorical covariates are needed for SAIGE-GENE and REGENIE. This parameter does not affect the Fisher's test branch at all	"sex"
	--variant_type_filter	true to use SNPs only, false otherwise	false
	--variant_freq_filter	this is an integer or floating point value. If the value is a float, then it is assumed to be minor allele frequency, while if it is an integer it is assumed to be minor allele count.	0.01
	--variant_missingness		0.05
	--protein_coding_genes_only	if you want to filter by protein coding genes	false
	--diff_missingness_pvalue		0.05
	--functional_annotation_filter_masks	The location of a json file containing functional annotation labels	"${projectDir}/input/functional_annotation_filter_masks.json"
	--mask_rank	The location of a json file ranking variant consequences	"${projectDir}/input/mask_rank.json"
	--run_saige_gene	Choose to run SAIGE-GENE	true
	--saige_masks		"LoF,LoF;missense"
	--run_regenie	Choose to run regenie	true
	--regenie_masks		"${projectDir}/input/regenie_masks.json"
	--run_fishers_test	Choose to run Rvtests/Fisher's test	true
	--rvtests_recessive_mode		false
	--rvtests_options	String containing any further options to pass to RVtests	"--siteMACMin 8 --single dominantExact"
	--output_file_name_suffix	This currently applies to output files in the Fisher's test branch only	"example_output"
Advanced inputs (unlikely to be changed)	--tracedir		"${params.outdir}"
	--genomic_data		"${projectDir}/input/aggV2_pgen_list_by_chromosomes_all_variants_biallelic_and_multiallelic.tsv"
	--vcf_files		"${projectDir}/input/aggV2_functional_annotations_list_by_chunks_VEP105.tsv"
	--precomputed_plink_files_for_grm_bed		"/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.bed"
	--precomputed_plink_files_for_grm_bim		"/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.bim"
	--precomputed_plink_files_for_grm_fam		"/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.fam"
	--consequence_severity_ranking_file		"${projectDir}/resources/VEP_severity_bcftools_translation_and_ranking.tsv"
	--ensembl_gene_list		"${projectDir}/resources/Ensembl_105_genes_coordinates_GRCh38.tsv"
	--ensembl_gene_list_protein_coding		"${projectDir}/resources/Ensembl_105_genes_coordinates_GRCh38_protein_coding.tsv"
Cluster settings (no real need to modify these)	--executor		'lsf'
	--cache		'lenient'
	--queue		{ task.attempt < 2 ? 'short' : 'medium' }
	--cpus		{ 1 + (task.attempt - 1) }
	--memory		{ 2.GB + (1.GB * (task.attempt - 1)) }
	--project_code		null
	--cluster_options		'-P null'
	--error_strategy		'retry'
	--max_retries		3
	--queue_size		5000
	--poll_interval		'30 sec'
	--exit_read_timeout		'30 sec'
Containers in the module_params scope (no need to modify these)	--bcftools_container		'docker-gel-research-containers.artifactory.aws.gel.ac/bcftools:v1.20'
	--bgenix_container		'docker-gel-research-containers.artifactory.aws.gel.ac/bgenix:v1.1.4.1'
	--plink2_container		'docker-gel-research-containers.artifactory.aws.gel.ac/plink:v1.90b7.6-v2.00-a516LM'
	--python_container		'docker-gel-research-containers.artifactory.aws.gel.ac/python:v3.12.6.1'
	--regenie_container		'docker-gel-research-containers.artifactory.aws.gel.ac/regenie:v3.4.1.1'
	--rvtests_container		'docker-gel-research-containers.artifactory.aws.gel.ac/rvtests:v2.1.0.2'
	--saige_container		'docker-gel-research-containers.artifactory.aws.gel.ac/saige:v1.3.6.1'