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AVT parametersΒΆ

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 "${projectDir}/input/chromosomes_subset.txt"
--exclusion_data_file a text file containing genomic regions to be excluded false
--input_cohort_file case/control cohort "/gel_data_resources/workflows/input_material/RDP_tools_aggregateVariantTestingWorkflow/auxiliary_files/input/cohort.txt"
--cohort_sample_column The column in your cohort file that specifies the platekey "Platekey"
--cohort_sex_column The column in your cohort file that specifies the sex "sex"
--control_coding How controls are coded in your input file 0
--phenotype_array List of columns in your input file that contain phenotype data "status"
--phenotype_type_array List of phenotype types that correspond to the list of phenotype columns "b"
--covariates List of columns of covariates in your input file "age,sex,age.age,age.sex,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20"
--categorical_covariates List of columns of discrete covariates in your input file "sex"
--variant_type_filter If you want to filter variants by consequences false
--variant_freq_filter this is an integer or floating point value. If the value is a float, then it is assumed to be minor allele frequency, while if it is an integer it is assumed to be minor allele count. 0.01
--variant_missingness 0.05
--protein_coding_genes_only if you want to filter by protein coding genes false
--diff_missingness_pvalue 0.05
--functional_annotation_filter_masks The location of a json file containing functional annotation labels "${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 [
"--siteMACMin 8",
"--single dominantExact"
]
--output_file_name_suffix this 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.tsv"
--vcf_files "${projectDir}/input/aggV2_functional_list.tsv"
--precomputed_plink_files_for_grm_bed "/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.bed"
--precomputed_plink_files_for_grm_bim "/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.bim"
--precomputed_plink_files_for_grm_fam "/gel_data_resources/main_programme/aggregation/aggregate_gVCF_strelka/aggV2/additional_data/HQ_SNPs/GELautosomes_LD_pruned_1kgp3Intersect_common_and_rare_for_AVT_mpv10.fam"
--consequence_severity_ranking_file "${projectDir}/resources/VEP_severity_bcftools_translation_and_ranking.tsv"
--ensembl_gene_list "${projectDir}/resources/Ensembl_105_genes_coordinates_GRCh38.tsv"
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:v1.16.1'
--bgenix_container 'docker-gel-research-containers.artifactory.aws.gel.ac/bgenix:v1.1.7'
--plink2_container 'docker-gel-research-containers.artifactory.aws.gel.ac/plink:v1.90b7.2-v2.00a6LM'
--python_container 'docker-gel-research-containers.artifactory.aws.gel.ac/python:v3.11.4.1'
--regenie_container 'docker-gel-research-containers.artifactory.aws.gel.ac/regenie:v3.3'
--rvtests_container 'docker-gel-research-containers-test.artifactory.aws.gel.ac/rvtests:v2.1.0'
--saige_container 'docker-gel-research-containers.artifactory.aws.gel.ac/saige:v1.3.0'