Rd_dna.pm

package MIP::Cli::Mip::Analyse::Rd_dna;

use 5.026;
use Carp;
use open qw{ :encoding(UTF-8) :std };
use utf8;
use warnings;
use warnings qw{ FATAL utf8 };

## CPANM
use autodie qw{ :all };
use MooseX::App::Command;
use MooseX::Types::Moose qw{ ArrayRef Bool HashRef Int Num Str };
use Moose::Util::TypeConstraints;

## MIPs lib
use MIP::Main::Analyse qw{ mip_analyse };

extends(qw{ MIP::Cli::Mip::Analyse });

command_short_description(q{Rare disease DNA analysis});

command_long_description(q{Rare disease DNA analysis on wes, wgs or mixed sequence data});

command_usage(q{mip <analyse> <rd_dna> <case_id> --config <config_file> });

## Define, check and get Cli supplied parameters
_build_usage();

sub run {
    my ($arg_href) = @_;

    ## Remove Moose::App extra variable
    delete $arg_href->{extra_argv};

    ## Input from Cli
    my %active_parameter = %{$arg_href};

    use MIP::Definition qw{ get_dependency_tree_from_definition_file
      get_first_level_keys_order_from_definition_file
      get_parameter_definition_file_paths
      get_parameter_from_definition_files };
    use MIP::Dependency_tree qw{ get_dependency_tree_chain set_dependency_tree_order };
    use MIP::Parameter qw{ get_cache get_order_of_parameters print_recipe };

    ## %parameter holds all defined parameters for MIP analyse rd_dna
    ## CLI commands inheritance level
    my $level = q{rd_dna};

    my %parameter = get_parameter_from_definition_files( { level => $level, } );

    my @rd_dna_definition_file_paths = get_parameter_definition_file_paths( { level => $level, } );

    ### To write parameters and their values to log in logical order
    ## Adds the order of first level keys from definition files to array
    my @order_parameters =
      get_order_of_parameters( { define_parameters_files_ref => \@rd_dna_definition_file_paths, } );

    ## Print recipes if requested and exit
    print_recipe(
        {
            order_parameters_ref => \@order_parameters,
            parameter_href       => \%parameter,
            print_recipe         => $active_parameter{print_recipe},
            print_recipe_mode    => $active_parameter{print_recipe_mode},
        }
    );

    ## Get dependency tree and store in parameter hash
    %{ $parameter{dependency_tree_href} } =
      get_dependency_tree_from_definition_file( { level => $level, } );

    ## Sets chain id to parameters hash from the dependency tree
    get_dependency_tree_chain(
        {
            dependency_tree_href => $parameter{dependency_tree_href},
            parameter_href       => \%parameter,
        }
    );

    ## Set order of recipes according to dependency tree
    set_dependency_tree_order(
        {
            dependency_tree_href => $parameter{dependency_tree_href},
            recipes_ref          => \@{ $parameter{cache}{order_recipes_ref} },
        }
    );

    ## File info hash
    my %file_info = (

        # BWA human genome reference file endings
        bwa_build_reference => [qw{ .bwt .ann .amb .pac .sa }],

        bwa_mem2_build_reference => [qw{ .0123 .ann .amb .bwt.2bit.64 .pac }],

        exome_target_bed => [qw{ .interval_list .pad100.interval_list }],

        # Human genome meta files
        human_genome_reference_file_endings => [qw{ .dict .fai }],

        # RTG human genome reference file endings
        rtg_vcfeval_reference_genome => [qw{ _sdf_dir }],
    );

    mip_analyse(
        {
            active_parameter_href => \%active_parameter,
            file_info_href        => \%file_info,
            order_parameters_ref  => \@order_parameters,
            parameter_href        => \%parameter,
        }
    );

    return;
}

sub _build_usage {

## Function : Get and/or set input parameters
## Returns  :
## Arguments:

    option(
        q{decompose_normalize_references} => (
            cmd_flag => q{dec_norm_ref},
            cmd_tags => [
q{gatk_baserecalibration_known_sites, gatk_haplotypecaller_snp_known_set, gatk_variantrecalibration_resource_snv, gatk_variantrecalibration_resource_indel, frequency_genmod_filter_1000g, gatk_varianteval_gold, gatk_varianteval_dbsnp}
            ],
            documentation => q{Set the references to be decomposed and normalized},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{exome_target_bed} => (
            cmd_tags      => [q{file.bed=Sample_id; Default: latest_supported_capturekit.bed}],
            documentation => q{Exome target bed file per sample id},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{expected_coverage} => (
            cmd_tags      => [q{sample_id=expected_coverage}],
            documentation => q{Expected median target coverage for analysis},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{variant_annotation} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate vcf},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{vcfanno_config} => (
            documentation => q{SNV/Indel vcfanno toml config},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{mt_annotation} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{MT annotation vcf},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{mt_annotation_offline} => (
            documentation => q{MT variants using offline-mode},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_disable_auto_index_and_file_lock} => (
            cmd_flag      => q{gatk_dis_auto_ind_fl},
            documentation => q{Disable auto index creation and locking when reading rods},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_path} => (
            documentation => q{Path to GATK directory},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{human_genome_reference} => (
            cmd_tags      => [q{Default: grch37_homo_sapiens_-d5-.fasta}],
            documentation => q{Human genome reference},
            is            => q{rw},
            isa           => Str,
        )
    );

    has(
        q{recipe_core_number} => (
            cmd_tags      => [q{recipe_name=X(cores)}],
            documentation => q{Set the number of cores for each recipe},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    has(
        q{recipe_gpu_number} => (
            cmd_tags      => [q{recipe_name=X(gpus)}],
            documentation => q{Set the number of gpus for each recipe},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{set_recipe_gpu_number} => (
            cmd_tags      => [q{recipe_name=X(gpus)}],
            documentation => q{Set the number of gpus for specific recipe(s)},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{gpu_capable_executables} => (
            cmd_flag      => q{gpu_capable_executables},
            documentation => q{List of executables with GPU capabilities},
            is            => q{rw},
            isa           => ArrayRef [ enum( [qw{ run_deepvariant call_variants }] ) ],
        )
    );

    has(
        q{recipe_memory} => (
            cmd_tags      => [q{recipe_name=X(G)}],
            documentation => q{Set the memory for each recipe},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    has(
        q{recipe_time} => (
            cmd_tags      => [q{recipe_name=time(hours)}],
            documentation => q{Set the time allocation for each recipe},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{infile_dirs} => (
            cmd_aliases   => [qw{ ifd }],
            cmd_tags      => [q{infile_dirs=sample_id}],
            documentation => q{Infile directory(s)},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{picardtools_path} => (
            documentation => q{Path to Picardtools},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gzip_fastq} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Gzip fastq files},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{fastqc_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Sequence quality analysis using FastQC},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{bwa_mem} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Align reads using Bwa Mem},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{bwa_mem2} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Align reads using Bwa mem 2},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{bwa_mem_bamstats} => (
            documentation => q{Collect statistics from BAM files},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{bwa_mem_cram} => (
            documentation => q{Use CRAM-format for additional output file},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{bwa_mem_hla} => (
            documentation => q{Apply HLA typing},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{bwa_mem_run_bwakit} => (
            documentation => q{Use bwakit when aligning to GRCh38},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{bwa_soft_clip_sup_align} => (
            documentation => q{Use soft clipping for supplementary alignments},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{deepvariant} => (
            documentation => q{Use deepvariant for variant calling},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{glnexus} => (
            documentation => q{Use glnexus to merge sample vcfs from deepvariant},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{samtools_merge} => (
            cmd_flag      => q{samtools_merge},
            cmd_tags      => [q{Analysis recipe switch}],
            documentation =>
              q{Merge (BAM file(s) ) or rename single samples for downstream processing},
            is  => q{rw},
            isa => enum( [ 1, 2 ] ),
        )
    );

    option(
        q{markduplicates} => (
            cmd_flag      => q{markduplicates},
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Markduplicate reads},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{markduplicates_picardtools_opt_dup_dist} => (
            cmd_flag      => q{picard_mdup_odd},
            cmd_tags      => [q{Default: 2500}],
            documentation => q{Picardtools markduplicates optical duplicate distance},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{gatk_baserecalibration} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Recalibration of bases using GATK BaseReCalibrator/PrintReads},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_baserecalibration_covariates} => (
            cmd_flag => q{gatk_baserecal_covariates},
            cmd_tags => [
q{Default: ReadGroupCovariate, ContextCovariate, CycleCovariate, QualityScoreCovariate}
            ],
            documentation => q{GATK BaseReCalibration covariates},
            is            => q{rw},
            isa           => ArrayRef [
                enum(
                    [
                        qw{ ContextCovariate CycleCovariate QualityScoreCovariate ReadGroupCovariate RepeatLengthCovariate RepeatUnitCovariate RepeatUnitAndLengthCovariate }
                    ]
                )
            ],
        )
    );

    option(
        q{gatk_baserecalibration_disable_indel_qual} => (
            cmd_flag      => q{gatk_baserecal_dis_indel_q},
            documentation => q{Disable indel quality scores},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_baserecalibration_known_sites} => (
            cmd_flag => q{gatk_baserecal_ks},
            cmd_tags => [
q{Default: grch37_dbsnp_-138-.vcf, grch37_1000g_indels_-phase1-.vcf, grch37_mills_and_1000g_indels_-gold_standard-.vcf}
            ],
            documentation => q{GATK BaseReCalibration known SNV and INDEL sites},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{gatk_baserecalibration_read_filters} => (
            cmd_flag      => q{gatk_baserecal_read_filts},
            cmd_tags      => [q{Default: OverclippedRead}],
            documentation => q{Filter out reads according to set filter},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{gatk_baserecalibration_static_quantized_quals} => (
            cmd_flag      => q{gatk_baserecal_sta_qua_qua},
            cmd_tags      => [q{Default: 10,20,30,40}],
            documentation => q{Static binning of base quality scores},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{gatk_collectreadcounts} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{GATK CollectReadCounts for Gens},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_denoisereadcounts} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{GATK DenoiseReadCounts for Gens},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gens_generatedata} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Generates .bed-files for Gens},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gens_intervals} => (
            cmd_tags      => [q{Default: grch37_gens_targets_preprocessed_100bp.interval_list}],
            documentation => q{Precomputed 100bp intervals for Gens},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gens_panel_of_normals_female} => (
            cmd_tags      => [q{Default: grch37_gens_female_pon_100bp.hdf5}],
            documentation => q{Gens read count reference},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gens_panel_of_normals_male} => (
            cmd_tags      => [q{Default: grch37_gens_male_pon_100bp.hdf5}],
            documentation => q{Gens read count reference},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gens_gnomad_positions} => (
            cmd_tags      => [q{Default: grch37_gnomad.genomes.r2.1.1.sites.5percent.pos.txt}],
            documentation => q{Gnomad SNV positions for Gens},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{chanjo_sexcheck} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Predicts gender from sex chromosome coverage},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{chanjo_sexcheck_log_level} => (
            cmd_flag      => q{chanjo_sexcheck_ll},
            documentation => q{Set chanjo sex log level},
            is            => q{rw},
            isa           => enum( [qw{ DEBUG INFO WARNING ERROR CRITICAL }] ),
        )
    );

    option(
        q{sambamba_depth} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Sambamba depth coverage analysis},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sambamba_depth_bed} => (
            documentation => q{Reference bed file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sambamba_depth_base_quality} => (
            cmd_flag      => q{sba_depth_bq},
            cmd_tags      => [q{Default: 10}],
            documentation => q{Do not count bases with lower base quality},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{sambamba_depth_cutoffs} => (
            cmd_flag      => q{sba_depth_co},
            documentation => q{Read depth cutoff},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{sambamba_depth_mapping_quality} => (
            cmd_flag      => q{sba_depth_mq},
            cmd_tags      => [q{Default: 10}],
            documentation => q{Do not count reads with lower mapping quality},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{sambamba_depth_mode} => (
            documentation => q{Mode unit to print the statistics on},
            is            => q{rw},
            isa           => enum( [qw{ base region window }] ),
        )
    );

    option(
        q{sambamba_depth_noduplicates} => (
            cmd_flag      => q{sba_depth_nod},
            documentation => q{Do not include duplicates in coverage calculation},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sambamba_depth_quality_control} => (
            cmd_flag      => q{sba_depth_qc},
            documentation => q{Do not include reads with failed quality control},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{smncopynumbercaller} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{SMN copy number analysis},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{star_caller} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{CYP2D6 allele analysis},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{telomerecat} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Telomere analysis},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{telomerecat_use_sample_id_as_display_name} => (
            cmd_tags      => [q{Default: 0}],
            documentation => q{Use sample id as display name for telomerecat outfile},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{tiddit_coverage} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Generate coverage data from alignment},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{picardtools_collectmultiplemetrics} => (
            cmd_flag      => q{ppt_col_mul_met},
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Qc metrics calculation},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{picardtools_collecthsmetrics} => (
            cmd_flag      => q{ppt_col_hs_met},
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Qc metrics calculation for capture},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{cnvnator_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Structural variant calling using CNVnator},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{cnv_bin_size} => (
            cmd_tags      => [q{Default: 1000}],
            documentation => q{CNVnator bin size},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{delly_call} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Structural variant calling using Delly},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{delly_reformat} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Merge, regenotype and filter using Delly},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{delly_exclude_file} => (
            cmd_tags      => [q{Default: hg19_human_excl_-0.7.6-.tsv}],
            documentation => q{Exclude centomere and telemore regions in delly calling},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{delly_types} => (
            cmd_tags      => [q{Default: DEL,DUP,INV,INS}],
            documentation => q{Type of SV to call},
            is            => q{rw},
            isa           => ArrayRef [ enum( [qw{ DEL DUP INV INS TRA }] ), ],
        )
    );

    option(
        q{expansionhunter} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Anaylse expansions of Short Tandem Repeats},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{expansionhunter_variant_catalog_file_path} => (
            cmd_flag      => q{exphun_var_cat_fp},
            documentation => q{Path to variant catalog json file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{manta} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Structural variant calling using Manta},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{manta_call_regions_file_path} => (
            documentation => q{Path to manta call regions file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{tiddit} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Structural variant calling using Tiddit},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{tiddit_coverage_bin_size} => (
            cmd_tags      => [q{Default: 500}],
            documentation => q{Size of coverage bins in calculation},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{tiddit_minimum_number_supporting_pairs} => (
            cmd_flag      => q{tid_min_num_sp},
            cmd_tags      => [q{Default: 6}],
            documentation => q{Minimum number of supporting reads},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{sv_combinevariantcallsets} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Combine structural variant call sets},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_combinevariantcallsets_bcf_file} => (
            cmd_flag      => q{sv_comb_vcs_bf},
            documentation => q{Produce a bcf from the CombineStructuralVariantCallSet vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_svdb_merge_prioritize} => (
            documentation => q{Prioritization order of structural variant callers},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_decompose} => (
            documentation => q{Split multi allelic records into single records},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_annotate} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate and filter structural variant calls},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_vcfanno_config} => (
            documentation => q{Structural variants vcfanno toml config},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_fqa_vcfanno_filters} => (
            documentation => q{Frequency annotations to use when filtering },
            is            => q{rw},
            isa           => ArrayRef,
        )
    );

    option(
        q{sv_frequency_filter} => (
            documentation => q{Remove common structural variants from vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_svdb_query} => (
            documentation => q{Annotate structural variants using svdb query},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_svdb_query_db_files} => (
            cmd_tags      => [q{file.vcf=vcf_info_key}],
            documentation => q{Database file(s) for annotation},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{sv_svdb_query_overlap} => (
            documentation => q{Database file(s) for annotation},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcf2cytosure_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation =>
q{Convert a VCF with structural variants to the “.CGH” format used by the commercial Cytosure software},
            is  => q{rw},
            isa => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{vcf2cytosure_blacklist} => (
            documentation => q{Exclude regions file path},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcf2cytosure_exclude_filter} => (
            cmd_flag      => q{vcf2cytosure_ex_fi},
            documentation => q{Filter vcf using bcftools exclude filter string},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcf2cytosure_freq} => (
            cmd_tags      => [q{Default: 0.01}],
            documentation => q{Specify maximum frequency},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{vcf2cytosure_freq_tag} => (
            cmd_tags      => [q{Default: FRQ}],
            documentation => q{Specify frequency tag},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcf2cytosure_maxbnd} => (
            cmd_tags      => [q{Default: 5000}],
            documentation => q{Specify maximum BND},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{vcf2cytosure_no_filter} => (
            documentation => q{Do not use any filtering},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{vcf2cytosure_var_size} => (
            cmd_tags      => [q{Default: 5000}],
            documentation => q{Specify minimum variant size},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{vcf2cytosure_use_sample_id_as_display_name} => (
            cmd_tags      => [q{Default: 0}],
            documentation => q{Use sample id as display name for vcf2cytosure outfile},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_varianteffectpredictor} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate SV variants using VEP},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_vep_features} => (
            cmd_tags => [
q{Default: hgvs, symbol, numbers, sift, polyphen, humdiv, domains, protein, ccds, uniprot, biotype, regulatory, tsl, canonical, per_gene, appris}
            ],
            documentation => q{VEP features},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{sv_vcfparser} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Parse structural variants using vcfParser.pl},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_vcfparser_add_all_mt_var} => (
            cmd_flag      => q{sv_vcfparser_all_mt},
            documentation => q{Add all MT variants in select vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_vcfparser_per_gene} => (
            documentation => q{Keep only most severe consequence per gene},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_vcfparser_range_feature_annotation_columns} => (
            cmd_flag      => q{sv_vcfparser_fac},
            documentation => q{Range annotations feature columns},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{sv_vcfparser_range_feature_file} => (
            cmd_flag      => q{sv_vcfparser_rff},
            cmd_tags      => [q{Format: tsv}],
            documentation => q{Range annotations file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_vcfparser_select_feature_annotation_columns} => (
            cmd_flag      => q{sv_vcfparser_slt_fac},
            documentation => q{Feature columns to use in annotation},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{sv_vcfparser_select_file} => (
            cmd_flag      => q{sv_vcfparser_slt_fl},
            cmd_tags      => [q{Format: tsv; HGNC Symbol required in file}],
            documentation => q{Select file with list of genes to analyse separately},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_vcfparser_select_file_matching_column} => (
            cmd_flag      => q{sv_vcfparser_slt_fmc},
            documentation => q{Position of HGNC Symbol column in select file},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{sv_vcfparser_vep_transcripts} => (
            cmd_flag      => q{sv_vcfparser_vtr},
            documentation => q{Parse VEP transcript specific entries},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_rankvariant} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Ranking of annotated SV variants},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_genmod_annotate_regions} => (
            cmd_flag      => q{sv_genmod_ann_reg},
            documentation =>
              q{Use predefined gene annotation supplied with genmod for defining genes},
            is  => q{rw},
            isa => Bool,
        )
    );

    option(
        q{sv_genmod_models_case_type} => (
            cmd_flag      => q{sv_genmod_mod_fam_typ},
            cmd_tags      => [q{Default: mip}],
            documentation => q{Use one of the known setups},
            is            => q{rw},
            isa           => enum( [qw{ped alt cmms mip}] ),
        )
    );

    option(
        q{sv_genmod_models_reduced_penetrance_file} => (
            cmd_flag      => q{sv_genmod_mod_red_pen_f},
            documentation => q{File containing genes with reduced penetrance},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_genmod_models_whole_gene} => (
            cmd_flag      => q{sv_genmod_mod_whl_gene},
            documentation => q{Allow compound pairs in intronic regions},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{sv_rank_model_file} => (
            documentation => q{Rank model config file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{sv_reformat} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Concatenating files},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{sv_reformat_remove_genes_file} => (
            cmd_flag      => q{sv_reformat_rem_gen_f},
            documentation => q{Remove variants with hgnc_ids from file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{me_merge_bam} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Prepare bam files for RetroSeq},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{retroseq} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Discover mobile elements using RetroSeq},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{me_merge_vcfs} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Merge sample vcfs from RetroSeq},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{me_merge_vcfs_bnd_distance} => (
            cmd_tags      => [q{Default: 150}],
            documentation => q{Maximum distance between two similar BNDs},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{me_merge_vcfs_overlap} => (
            cmd_tags      => [q{Default: }],
            documentation => q{Overlap required to merge two events},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{mobile_element_reference} => (
            cmd_tags      => [q{file.vcf=TE_type}],
            documentation => q{Database file(s) for mobile element iscovery},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{me_annotate} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate mobile elememnt},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{me_annotate_query_bnd_distance} => (
            cmd_tags      => [q{Default: 150}],
            documentation => q{Maximum distance between two similar BNDs},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{me_annotate_query_overlap} => (
            cmd_tags      => [q{Default: }],
            documentation => q{Overlap required to annotate},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{me_varianteffectpredictor} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate mobile elements with VEP},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{me_filter} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Filter mobile elements},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{me_filter_frequency_threshold} => (
            cmd_tags      => [q{Default: 0.1}],
            documentation =>
              q{Threshold frequency for variants to be filtered out, set to 0 to disable},
            is  => q{rw},
            isa => Num,
        )
    );

    option(
        q{gatk_haplotypecaller} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Variant discovery using GATK HaplotypeCaller},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_haplotypecaller_annotation} => (
            cmd_flag => q{gatk_haplotype_ann},
            cmd_tags => [
q{Default: BaseQualityRankSumTest, ChromosomeCounts, Coverage, DepthPerAlleleBySample, FisherStrand, MappingQualityRankSumTest, QualByDepth, RMSMappingQuality, ReadPosRankSumTest, StrandOddsRatio}
            ],
            documentation => q{GATK HaploTypeCaller annotations},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{gatk_haplotypecaller_emit_ref_confidence} => (
            cmd_flag      => q{gatk_haplotype_emit_ref_conf},
            cmd_tags      => [q{Default: GVCF}],
            documentation => q{VCF to produce},
            is            => q{rw},
            isa           => ArrayRef [ enum( [qw{ NONE BP_RESOLUTION GVCF }] ), ],
        )
    );

    option(
        q{gatk_haplotypecaller_linked_de_bruijn_graph} => (
            cmd_flag      => q{gatk_haplotype_lk_bruijn_grh},
            documentation => q{Use linked de bruijn graph in the variant calling},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_haplotypecaller_no_soft_clipped_bases} => (
            cmd_flag      => q{gatk_haplotype_no_soft_cb},
            documentation => q{Do not include soft clipped bases in the variant calling},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_haplotypecaller_pcr_indel_model} => (
            cmd_flag      => q{gatk_haplotype_pcr_ind_mod},
            cmd_tags      => [q{Default: NONE; Set to "0" to disable}],
            documentation => q{PCR indel model to use},
            is            => q{rw},
            isa => ArrayRef [ enum( [ 0, qw{ AGGRESSIVE CONSERVATIVE HOSTILE NONE } ] ), ],
        )
    );

    option(
        q{gatk_haplotypecaller_snp_known_set} => (
            cmd_flag      => q{gatk_haplotype_snp_ks},
            cmd_tags      => [q{Default: grch37_dbsnp_-138-.vcf}],
            documentation => q{GATK HaplotypeCaller dbSNP set for annotating ID columns},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gatk_genotypegvcfs} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Merge gVCF records using GATK GenotypeGVCFs},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_genotypegvcfs_ref_gvcf} => (
            cmd_flag      => q{gatk_genotype_ref_gvcf},
            documentation => q{GATK GenoTypeGVCFs gVCF reference infile list for joint genotyping},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gatk_genotypegvcfs_all_sites} => (
            cmd_flag      => q{gatk_genotype_all_sit},
            documentation => q{Include loci found to be non-variant after genotyping},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_gathervcfs} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Concatenate gVCF records using GATK Concatenate variants},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_gathervcfs_bcf_file} => (
            cmd_flag      => q{gatk_genotype_bcf_f},
            documentation => q{Produce a bcf from the GATK ConcatenateGenoTypeGVCFs vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation =>
              q{Variant recalibration using GATK VariantRecalibrator/ApplyRecalibration},
            is  => q{rw},
            isa => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_variantrecalibration_annotations} => (
            cmd_flag      => q{gatk_varrecal_ann},
            cmd_tags      => [q{Default: QD, MQRankSum, ReadPosRankSum, FS, SOR, DP}],
            documentation => q{Annotations to use with GATK VariantRecalibrator},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{gatk_calculategenotypeposteriors} => (
            cmd_flag      => q{gatk_calculategenotypeposteriors},
            documentation => q{Perform gatk calculate genotype posterior},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_cnnscorevariants} => (
            cmd_flag      => q{gatk_cnnscorevariants},
            documentation =>
              q{Perform gatk cnnscorevariants instead of gatk variantscore recalibration},
            is  => q{rw},
            isa => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration_dp_annotation} => (
            cmd_flag      => q{gatk_varrecal_dp_ann},
            documentation => q{Use the DP annotation in variant recalibration},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration_indel_max_gaussians} => (
            cmd_flag      => q{gatk_varrecal_indel_max_gau},
            documentation => q{Use hard filtering for indels},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration_indel_tsfilter_level} => (
            cmd_flag      => q{gatk_varrecal_indel_ts_fl},
            cmd_tags      => [q{Defaults: 99.9}],
            documentation => q{Truth sensitivity level for indels at which to start filtering},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{gatk_variantrecalibration_keep_unnormalised} => (
            cmd_flag      => q{gatk_variantrecalibration_keep_unn},
            documentation => q{Do not normalise variants},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration_resource_indel} => (
            cmd_flag => q{gatk_varrecal_res_indel},
            cmd_tags => [
q{file.vcf=settings; Default: grch37_dbsnp_-138-.vcf="dbsnp,known=true,training=false,truth=false,prior=2.0", grch37_mills_and_1000g_indels_-gold_standard-.vcf="mills,VCF,known=true,training=true,truth=true,prior=12.0"}
            ],
            documentation => q{Resource to use with GATK VariantRecalibrator in INDEL|BOTH},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{gatk_variantrecalibration_resource_snv} => (
            cmd_flag => q{gatk_varrecal_res_snv},
            cmd_tags => [
q{file.vcf=settings; Default: grch37_dbsnp_-138-.vcf="dbsnp,known=true,training=false,truth=false,prior=2.0", grch37_hapmap_-3.3-.vcf="hapmap,VCF,known=false,training=true,truth=true,prior=15.0", grch37_1000g_omni_-2.5-.vcf="omni,VCF,known=false,training=true,truth=false,prior=12.0", grch37_1000g_snps_high_confidence_-phase1-.vcf="1000G,known=false,training=true,truth=false,prior=10.0"}
            ],
            documentation => q{Resource to use with GATK VariantRecalibrator in SNV|BOTH mode},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{gatk_variantrecalibration_snv_max_gaussians} => (
            cmd_flag      => q{gatk_varrecal_snv_max_gau},
            documentation => q{Use hard filtering for snvs},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_variantrecalibration_snv_tsfilter_level} => (
            cmd_flag      => q{gatk_varrecal_snv_ts_fl},
            cmd_tags      => [q{Defaults: 99.9}],
            documentation => q{Truth sensitivity level for snvs at which to start filtering},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{gatk_variantrecalibration_ts_tranches} => (
            documentation => q{Tranches to slice data},
            is            => q{rw},
            isa           => ArrayRef,
        )
    );

    option(
        q{gatk_variantrecalibration_trust_all_polymorphic} => (
            cmd_flag      => q{gatk_varrecal_trust_poly},
            documentation => q{Trust all training sites to be polymorphic},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_num_reference_samples_if_no_call} => (
            cmd_flag      => q{gatk_num_ref_sam_if_ncall},
            cmd_tags      => [q{Defaults: 7854}],
            documentation =>
q{Number of hom-ref genotypes to infer at sites not present in a panel. Connected to option 'gatk_calculate_genotype_call_set'},
            is  => q{rw},
            isa => Int,
        )
    );

    option(
        q{gatk_calculate_genotype_call_set} => (
            cmd_flag      => q{gatk_calc_gtype_cs},
            cmd_tags      => [q{Defaults: grch37_gnomad.genomes_-r2.0.1-.vcf.gz}],
            documentation => q{Callset to use in calculating genotype priors},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gatk_combinevariantcallsets} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Combine variant call sets},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_combinevariantcallsets_bcf_file} => (
            cmd_flag      => q{gatk_combinevar_bcf_f},
            documentation => q{Produce a bcf from the GATK CombineVariantCallSet vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{gatk_combinevariants_genotype_merge_option} => (
            cmd_flag      => q{gatk_combinevar_merge_opt},
            cmd_tags      => [q{Defaults: PRIORITIZE}],
            documentation => q{Type of merge to perform},
            is            => q{rw},
            isa           => enum( [qw{ UNIQUIFY PRIORITIZE UNSORTED REQUIRE_UNIQUE }] ),
        )
    );

    option(
        q{gatk_combinevariants_prioritize_caller} => (
            cmd_flag      => q{gatk_combinevar_prio_cal},
            documentation => q{Prioritization order of variant callers},
            is            => q{rw},
            isa => enum( [ q{deepvariant,haplotypecaller}, q{haplotypecaller,deepvariant} ] ),
        )
    );

    option(
        q{gatk_combinevariants_callers_to_combine} => (
            cmd_flag      => q{gatk_combinevar_use_callers},
            documentation => q{Combine vcf output from these recipes},
            cmd_tags      => [q{Defaults: glnexus_merge}],
            is            => q{rw},
            isa           => ArrayRef [ enum( [qw{ gatk_variantrecalibration glnexus_merge }] ), ],
        )
    );

    option(
        q{gatk_variantevalall} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Variant evaluation using GATK varianteval for all variants},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_variantevalexome} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Variant evaluation using GATK varianteval for exonic variants},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{gatk_varianteval_dbsnp} => (
            cmd_tags      => [q{Default: dbsnp_grch37_138_esa_129.vcf}],
            documentation => q{DbSNP file used in GATK varianteval},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{gatk_varianteval_gold} => (
            cmd_tags      => [q{Default: grch37_mills_and_1000g_indels_-gold_standard-.vcf}],
            documentation => q{Gold indel file used in GATK varianteval},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{prepareforvariantannotationblock} => (
            cmd_flag      => q{prep_for_var_ann_bl},
            cmd_tags      => [q{Analysis recipe switch}],
            documentation =>
              q{Prepare for variant annotation block by copying and splitting files per contig},
            is  => q{rw},
            isa => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{rhocall_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Rhocall performs annotation of variants in autozygosity regions},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{rhocall_frequency_file} => (
            cmd_tags      => [q{Default: grch37_anon_swegen_snp_-2016-10-19-.tab.gz; tsv}],
            documentation => q{Frequency file for bcftools roh calculation},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{bcftools_norm} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Decompose and normalize},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{bcftools_missing_alt_allele} => (
            documentation => q{Remove missing alternative alleles '*'},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{bcftools_normalize} => (
            documentation => q{Normalize variants},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{rhocall_viz} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Create roh files needed for chromograph},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{upd_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Create bed files needed for chromograph},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{chromograph_cov} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Chromograph coverage},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{chromograph_rhoviz} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Chromograph on rhocall_viz output},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{chromograph_upd} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Chromograph on upd output},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{frequency_filter} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Filter variants on frequency},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{fqf_annotations} => (
            documentation => q{Frequency annotations to use when filtering },
            is            => q{rw},
            isa           => ArrayRef,
        )
    );

    option(
        q{fqf_bcftools_filter_threshold} => (
            cmd_flag      => q{freq_bcftools_fil_trh},
            cmd_tags      => [q{Default: 0.10}],
            documentation => q{Threshold for filtering variants},
            is            => q{rw},
            isa           => Num,
        )
    );

    option(
        q{cadd_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate variants with CADD},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{cadd_column_names} => (
            documentation => q{Column names in cadd tsv},
            is            => q{rw},
            isa           => ArrayRef,
        )
    );

    option(
        q{cadd_vcf_header_file} => (
            documentation => q{},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{varianteffectpredictor} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Annotate variants using VEP},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{vep_custom_annotation} => (
            documentation => q{VEP custom annotation},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{vep_directory_cache} => (
            documentation => q{Specify the cache directory to use},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vep_features} => (
            cmd_tags => [
q{Default: hgvs, symbol, numbers, sift, polyphen, humdiv, domains, protein, ccds, uniprot, biotype, regulatory, tsl, canonical, per_gene, appris}
            ],
            documentation => q{VEP features},
            is            => q{rw},
            isa           => ArrayRef [Str],
        )
    );

    option(
        q{vep_plugins_dir_path} => (
            documentation => q{Path to directory with VEP plugins},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcfparser_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Parse structural variants using vcfParser.pl},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{vcfparser_add_all_mt_var} => (
            cmd_flag      => q{vcfparser_all_mt},
            documentation => q{Add all MT variants in select vcf},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{vcfparser_pli_score_file} => (
            cmd_tags      => [q{Format: tsv}],
            documentation => q{Gene pLI score file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcfparser_range_feature_annotation_columns} => (
            cmd_flag      => q{vcfparser_fac},
            documentation => q{Range annotations feature columns},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{vcfparser_range_feature_file} => (
            cmd_flag      => q{vcfparser_rff},
            cmd_tags      => [q{Format: tsv}],
            documentation => q{Range annotations file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcfparser_select_file} => (
            cmd_flag      => q{vcfparser_slt_fl},
            cmd_tags      => [q{Format: tsv; HGNC Symbol required in file}],
            documentation => q{Select file with list of genes to analyse separately},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{vcfparser_select_feature_annotation_columns} => (
            cmd_flag      => q{vcfparser_slt_fac},
            documentation => q{Feature columns to use in annotation},
            is            => q{rw},
            isa           => ArrayRef [Int],
        )
    );

    option(
        q{vcfparser_select_file_matching_column} => (
            cmd_flag      => q{vcfparser_slt_fmc},
            documentation => q{Position of HGNC Symbol column in select file},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{vcfparser_vep_transcripts} => (
            cmd_flag      => q{vcfparser_vtr},
            documentation => q{Parse VEP transcript specific entries},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{rankvariant} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Ranking of annotated variants},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{genmod_annotate_regions} => (
            cmd_flag      => q{genmod_ann_reg},
            documentation =>
              q{Use predefined gene annotation supplied with genmod for defining genes},
            is  => q{rw},
            isa => Bool,
        )
    );

    option(
        q{genmod_models_case_type} => (
            cmd_flag      => q{genmod_mod_fam_typ},
            cmd_tags      => [q{Default: mip}],
            documentation => q{Use one of the known setups},
            is            => q{rw},
            isa           => enum( [qw{ped alt cmms mip}] ),
        )
    );

    option(
        q{genmod_models_reduced_penetrance_file} => (
            cmd_flag      => q{genmod_mod_red_pen_f},
            documentation => q{File containing genes with reduced penetrance},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{genmod_models_whole_gene} => (
            cmd_flag      => q{genmod_mod_whl_gene},
            documentation => q{Allow compound pairs in intronic regions},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{rank_model_file} => (
            documentation => q{Rank model config file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{endvariantannotationblock} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{End variant annotation block by concatenating files},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{endvariantannotationblock_remove_genes_file} => (
            cmd_flag      => q{endvarannbl_rem_gen_f},
            documentation => q{Remove variants with hgnc_ids from file},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{peddy_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{QC for familial-relationships and sexes},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{plink} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{QC for samples gender and relationship},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{rtg_vcfeval} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Compare concordance with benchmark data set},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{nist_call_set_vcf} => (
            cmd_tags      => [q{Nist call set vcf information hash}],
            documentation => q{NIST high-confidence variant calls vcf},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{nist_call_set_bed} => (
            cmd_tags      => [q{Nist call set bed information hash}],
            documentation => q{NIST high-confidence variant calls bed},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{nist_id} => (
            cmd_tags      => [q{sample_id=nist_id}],
            documentation => q{Map sample_id to nist_id},
            is            => q{rw},
            isa           => HashRef,
        )
    );

    option(
        q{nist_versions} => (
            cmd_tags      => [q{Default: [2.19, 3.3.2]}],
            documentation => q{Map sample_id to nist_id},
            is            => q{rw},
            isa           => ArrayRef,
        )
    );

    option(
        q{qccollect_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Collect QC metrics from recipes output},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{qccollect_eval_metric_file} => (
            cmd_tags      => [q{Default: qc_eval_metric_-v1.3-.yaml}],
            documentation => q{File containing Qccollect evaluation metrics},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{qccollect_regexp_file} => (
            cmd_tags      => [q{Default: qc_regexp_-v1.25-.yaml}],
            documentation =>
q{Regular expression file containing the regular expression to be used for each program},
            is  => q{rw},
            isa => Str,
        )
    );

    option(
        q{qccollect_sampleinfo_file} => (
            cmd_tags      => [q{Default: {outdata_dir}/{case_id}/{case_id}_qc_sample_info.yaml}],
            documentation =>
              q{Sample info file containing info on what to parse from this analysis run},
            is  => q{rw},
            isa => Str,
        )
    );

    option(
        q{qccollect_skip_evaluation} => (
            documentation => q{Skip evaluation step in qccollect},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{qccollect_store_metrics_outfile} => (
            cmd_tags      => [q{Default: {outdata_dir}/{case_id}_metrics_deliverables.yaml}],
            documentation => q{File containing metrics from this analysis run},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{multiqc_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Create aggregate bioinformatics analysis report across many samples},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{multiqc_per_sample} => (
            documentation => q{Generate sample specific reports},
            is            => q{rw},
            isa           => Bool,
        )
    );

    option(
        q{samtools_subsample_mt} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Subsample the mitochondria reads},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{samtools_subsample_mt_depth} => (
            cmd_tags      => [q{Default: 60}],
            documentation => q{Set approximate coverage of subsampled bam file},
            is            => q{rw},
            isa           => Int,
        )
    );

    option(
        q{varg_ar} => (
            cmd_tags      => [q{Analysis recipe switch}],
            documentation => q{Compare resulting SVs and SNVs with positive controls},
            is            => q{rw},
            isa           => enum( [ 0, 1, 2 ] ),
        )
    );

    option(
        q{varg_truth_set_vcf} => (
            cmd_tags      => [q{Format: vcf}],
            documentation => q{vcf with expected SVs and SNVs},
            is            => q{rw},
            isa           => Str,
        )
    );

    option(
        q{isolate_singularity_containers} => (
            cmd_tags      => [q{Contain these containers}],
            documentation =>
              q{Run these singularity executables with --no-home and --cleanenv option},
            is  => qw{rw},
            isa => ArrayRef,
        )
    );

    return;
}

1;