<commit_before>---
## Version: 2.1.0
decompose_normalize_references:
  associated_program:
   - mip
  data_type: ARRAY
  default:
   - gatk_baserecalibration_known_sites
   - gatk_haplotypecaller_snp_known_set
   - gatk_variantrecalibration_resource_indel
   - frequency_genmod_filter_1000g
   - sv_vcfanno_config_file
   - gatk_varianteval_gold
   - gatk_varianteval_dbsnp
   - snpsift_annotation_files
  element_separator: ,
  type: mip
exome_target_bed:
  associated_program:
   - picardtools_collecthsmetrics
   - gatk_baserecalibration
   - gatk_haplotypecaller
  build_file: 1
  data_type: HASH
  exists_check: file
  reference: reference_dir
  type: path
expected_coverage:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
## genomeAnalysisToolKitPath
## GATK FTP Bundle Download version. Needed for all programs that download the human genome reference
gatk_bundle_download_version:
  associated_program:
   - bwa_mem
   - gatk_baserecalibration
   - cnvnator
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs 
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  data_type: SCALAR
  default: 2.8
  type: program_argument
gatk_downsample_to_coverage:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 1000
  type: program_argument
gatk_logging_level:
  associated_program:
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - cnvnator
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - rankvariant
  data_type: SCALAR
  default: INFO
  type: program_argument
gatk_path:
  associated_program:
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - rankvariant
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
genomic_set:
  associated_program:
   - mip
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## HumanGenomeReference
human_genome_reference:
  associated_program:
   - mip
   - bwa_mem
   - expansionhunter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - bcftools_mpileup
   - freebayes
   - manta
   - delly_call
   - cnvnator
   - tiddit
   - gatk_variantrecalibration
   - vt
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  data_type: SCALAR
  default: GRCh37_homo_sapiens_-d5-.fasta
  exists_check: file
  reference: reference_dir
  type: path
human_genome_reference_file_endings:
  associated_program:
   - bwa_mem
   - expansionhunter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - bcftools_mpileup
   - freebayes
   - manta
   - delly_call
   - cnvnator
   - tiddit
   - gatk_variantrecalibration
   - vt
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  build_file: 1
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## java large pages - affects all modules using java
java_use_large_pages:
  associated_program:
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - snpeff
  data_type: SCALAR
  default: 0
  type: program_argument
####Bash
module_core_number:
  associated_program:
   - mip
  data_type: HASH
  default:
    analysisrunstatus: 1
    bcftools_mpileup: 16
    bedtools_genomecov: 1
    bwa_mem: 16
    chanjo_sexcheck: 1
    cnvnator: 16
    delly_call: 16
    delly_reformat: 16
    endvariantannotationblock: 1
    evaluation: 1
    expansionhunter: 1
    fastqc: 0
    freebayes: 16
    frequency_filter: 16
    gatk_baserecalibration: 16
    gatk_combinevariantcallsets: 1
    gatk_genotypegvcfs: 2
    gatk_gathervcfs: 2
    gatk_haplotypecaller: 16
    gatk_variantevalall: 1
    gatk_variantevalexome: 1
    gatk_variantrecalibration: 2
    gzip_fastq: 0
    manta: 16
    markduplicates: 16
    multiqc: 1
    peddy: 4
    picardtools_collecthsmetrics: 2
    picardtools_collectmultiplemetrics: 2
    picardtools_mergesamfiles: 16
    plink: 1
    qccollect: 1
    rcovplots: 1
    rtg_vcfeval: 1
    sacct: 1
    sambamba_depth: 2
    samtools_subsample_mt: 1
    split_fastq_file: 4
    sv_annotate: 1
    sv_combinevariantcallsets: 1
    sv_rankvariant: 16
    sv_reformat: 1
    sv_varianteffectpredictor: 16
    sv_vcfparser: 16
    variant_integrity: 1
    vcf2cytosure: 1
  type: mip
module_time:
  associated_program:
   - mip
  data_type: HASH
  default:
    analysisrunstatus: 1
    bwa_mem: 30
    bcftools_mpileup: 40
    bedtools_genomecov: 15
    chanjo_sexcheck: 2
    cnvnator: 5
    delly_call: 10
    delly_reformat: 7
    endvariantannotationblock: 2
    evaluation: 1
    expansionhunter: 1
    fastqc: 10
    freebayes: 20
    frequency_filter: 2
    gatk_baserecalibration: 20
    gatk_combinevariantcallsets: 2
    gatk_genotypegvcfs: 10
    gatk_gathervcfs: 2
    gatk_haplotypecaller: 30
    gatk_variantevalall: 2
    gatk_variantevalexome: 2
    gatk_variantrecalibration: 10
    gzip_fastq: 2
    manta: 10
    markduplicates: 20
    multiqc: 1
    peddy: 1
    picardtools_collecthsmetrics: 10
    picardtools_collectmultiplemetrics: 10
    picardtools_mergesamfiles: 20
    plink: 1
    prepareforvariantannotationblock: 5
    qccollect: 1
    rankvariant: 10
    rcovplots: 1
    rhocall: 5
    rtg_vcfeval: 1
    sacct: 1
    sambamba_depth: 10
    samtools_subsample_mt: 1
    split_fastq_file: 10
    snpeff: 10
    sv_annotate: 2
    sv_combinevariantcallsets: 2
    sv_rankvariant: 2
    sv_reformat: 1
    sv_varianteffectpredictor: 10
    sv_vcfparser: 2
    tiddit: 10
    varianteffectpredictor: 10
    variant_integrity: 1
    vcfparser: 5
    vt: 10
    vcf2cytosure: 10
  type: mip
infile_dirs:
  associated_program:
   - mip
  exists_check: directory
  data_type: HASH
  type: path
  update_path: absolute_path
## Choosen MIP Aligner
outaligner_dir:
  associated_program:
   - mip
  data_type: SCALAR
  mandatory: no
  type: mip
picardtools_path:
  associated_program:
   - bwa_mem
   - picardtools_mergesamfiles
   - markduplicates
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
   - prepareforvariantannotationblock
   - delly_reformat
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
reduce_io:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  type: mip
replace_iupac:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  type: mip
###Programs
split_fastq_file:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  outfile_suffix: ".fastq.gz"
  program_name_path:
   - pigz
   - split
  type: program
split_fastq_file_read_batch:
  associated_program:
   - split_fastq_file
  data_type: SCALAR
  default: 25000000
  type: program_argument
## Gzip
gzip_fastq:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 1
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  program_name_path:
   - gzip
  type: program
## FastQC
fastqc:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  program_name_path:
   - fastqc
  type: program
## BWA
bwa_mem:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _sorted
  outfile_suffix: ".bam"
  outdir_name: bwa
  program_name_path:
   - bwa
   - samtools
   - sambamba
  program_type: aligners
  type: program
bwa_build_reference:
  associated_program:
   - bwa_mem
  build_file: 1
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
bwa_mem_bamstats:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 1
  type: program_argument
bwa_mem_cram:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 0
  type: program_argument
bwa_mem_hla:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 0
  type: program_argument
bwa_sambamba_sort_memory_limit:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 32G
  type: program_argument
## BAMCalibrationBlock
bamcalibrationblock:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  reduce_io: 1
  type: program
picardtools_mergesamfiles:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  type: program
markduplicates:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _md
  program_name_path:
   - sambamba
  type: program
markduplicates_picardtools_markduplicates:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 0
  type: program_argument
markduplicates_sambamba_markdup:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 0
  type: program_argument
markduplicates_sambamba_markdup_hash_table_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 262144
  type: program_argument
markduplicates_sambamba_markdup_io_buffer_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 2048
  type: program_argument
markduplicates_sambamba_markdup_overflow_list_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 200000
  type: program_argument
## GATK BAM Calibration
gatk_baserecalibration:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _brecal
  program_name_path:
   - gatk
  type: program
gatk_baserecalibration_known_sites:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - GRCh37_dbsnp_-138-.vcf
   - GRCh37_1000g_indels_-phase1-.vcf
   - GRCh37_mills_and_1000g_indels_-gold_standard-.vcf
  exists_check: file
  reference: reference_dir
  type: path
gatk_baserecalibration_read_filters:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - OverclippedReadFilter
  type: program_argument
gatk_baserecalibration_static_quantized_quals:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  default:
   - 10
   - 20
   - 30
   - 40
  type: program_argument
## Coverage Analysis
chanjo_sexcheck:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _sex
  outfile_suffix: ".tsv"
  program_name_path:
   - chanjo
  type: program
chanjo_sexcheck_log_level:
  associated_program:
   - chanjo_sexcheck
  data_type: SCALAR
  default: DEBUG
  type: program_argument
samtools_subsample_mt:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _subsample_MT
  outfile_suffix: ".bam"
  program_name_path: 
   - samtools
  type: program
samtools_subsample_mt_depth:
  analysis_mode: sample
  associated_program:
   - samtools_subsample_mt
  data_type: SCALAR
  default: 60
  type: program_argument
sambamba_depth:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _coverage
  outfile_suffix: ".bed"
  program_name_path:
   - sambamba
  type: program
sambamba_depth_base_quality:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 10
  type: program_argument
sambamba_depth_bed:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sambamba_depth_cutoffs:
  associated_program:
   - sambamba_depth
  element_separator: ,
  data_type: ARRAY
  default:
   - 10
   - 15
   - 20
   - 50
   - 100
  type: program_argument
sambamba_depth_mode:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: region
  type: program_argument
sambamba_depth_noduplicates:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 0
  type: program_argument
sambamba_depth_mapping_quality:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 10
  type: program_argument
sambamba_depth_quality_control:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 1
  type: program_argument
bedtools_genomecov:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _genomecov
  program_name_path:
   - bedtools
  type: program
bedtools_genomecov_max_coverage:
  associated_program:
   - bedtools_genomecov
  data_type: SCALAR
  default: 30
  type: program_argument
picardtools_collectmultiplemetrics:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  type: program
picardtools_collecthsmetrics:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _collecthsmetrics
  type: program
rcovplots:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  type: program
## Structural Variant Calling
cnvnator:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _cnvnator
  outdir_name: cnvnator
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - cnvnator
   - samtools
  program_type: structural_variant_callers
  type: program
cnv_bin_size:
  associated_program:
   - cnvnator
  data_type: SCALAR
  default: 1000
  type: program_argument
delly_call:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _dellycall
  program_name_path:
   - delly
  outdir_name: delly
  outfile_suffix: ".bcf"
  type: program
delly_reformat:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _dellyreformat
  program_name_path:
   - delly
   - bcftools
  outdir_name: delly
  outfile_suffix: ".vcf"
  program_type: structural_variant_callers
  type: program
delly_exclude_file:
  associated_program:
   - delly_call
   - delly_reformat
  data_type: SCALAR
  default: hg19_human_excl_-0.7.6-.tsv
  exists_check: file
  reference: reference_dir
  type: path
delly_types:
  associated_program:
   - delly_call
   - delly_reformat
  element_separator: ,
  data_type: ARRAY
  default:
   - DEL
   - DUP
   - INV
   - INS
  type: program_argument
expansionhunter:
  analysis_mode: sample
  associated_program:  
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _exphun
  outdir_name: expansionhunter
  outfile_suffix: ".vcf"
  program_name_path:
   - ExpansionHunter
  program_type: structural_variant_callers
  type: program
expansionhunter_repeat_specs_dir:
  associated_program:
   - expansionhunter
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
manta:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _manta
  program_name_path:
   - configManta.py
  outdir_name: manta
  outfile_suffix: ".vcf"
  program_type: structural_variant_callers
  type: program
tiddit:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _tiddit
  outdir_name: tiddit
  outfile_suffix: ".vcf"
  coverage_file_suffix: ".tab"
  program_name_path:
   - TIDDIT.py
  program_type: structural_variant_callers
  type: program
tiddit_bin_size:
  associated_program:
   - vcf2cytosure
   - tiddit
  data_type: SCALAR
  default: 500
  type: program_argument
tiddit_minimum_number_supporting_pairs:
  associated_program:
   - tiddit
  data_type: SCALAR
  default: 6
  type: program_argument
sv_combinevariantcallsets:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _comb_
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - svdb
   - vt
  type: program
sv_combinevariantcallsets_bcf_file:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  default: 0
  type: program_argument
sv_svdb_merge_prioritize:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  mandatory: no
  type: program_argument
sv_vt_decompose:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  default: 0
  type: program_argument
sv_annotate:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ann_
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - svdb
  type: program
sv_bcftools_view_filter:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_filter:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_filter_threshold:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0.10
  type: program_argument
sv_genmod_filter_1000g:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: GRCh37_all_wgs_-phase3_v5b.2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
sv_svdb_query:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_svdb_query_db_files:
  associated_program:
   - sv_annotate
  data_type: HASH
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_vcfannotation_header_lines_file:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno_config:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno_config_file:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: GRCh37_all_sv_-phase3_v2.2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
  type: program_argument
sv_vcfanno_lua:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
vcf2cytosure:
  analysis_mode: family
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: cyto_
  outfile_suffix: ".cgh"
  outdir_name: vcf2cytosure
  program_name_path:
    - TIDDIT.py
    - vcf2cytosure
    - bcftools
  type: program
vcf2cytosure_exclude_filter:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: ""
  type: program_argument
vcf2cytosure_freq:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0.01
  type: program_argument
vcf2cytosure_freq_tag:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: FRQ
  type: program_argument
vf2cytosure_no_filter:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0
  type: program_argument
vcf2cytosure_var_size:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0
  type: program_argument
sv_varianteffectpredictor:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: vep_
  program_name_path:
   - vep
  type: program
sv_vep_features:
  associated_program:
   - sv_varianteffectpredictor
  element_separator: ,
  data_type: ARRAY
  default:
   - hgvs
   - symbol
   - numbers
   - humdiv
   - domains
   - protein
   - ccds
   - uniprot
   - biotype
   - regulatory
   - tsl
   - canonical
   - per_gene
   - appris
   - cache
   - force_overwrite
   - no_progress
   - offline
  type: program_argument
sv_vep_plugins:
  associated_program:
   - sv_varianteffectpredictor
  element_separator: ,
  data_type: ARRAY
  default:
   - LoFtool
  type: program_argument
sv_vcfparser:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: parsed_
  type: program
sv_vcfparser_range_feature_annotation_columns:
  associated_program:
   - sv_vcfparser
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  type: program_argument
sv_vcfparser_range_feature_file:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
sv_vcfparser_outfile_count:
  associated_program:
   - sv_vcfparser
   - mip
  data_type: SCALAR
  default: 1
  type: program_argument
sv_vcfparser_per_gene:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  default: 0
  type: program_argument
sv_vcfparser_select_feature_annotation_columns:
  associated_program:
   - sv_vcfparser
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  type: program_argument
sv_vcfparser_select_file:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  exists_check: file
  type: path
  update_path: absolute_path
sv_vcfparser_select_file_matching_column:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  type: program_argument
sv_vcfparser_vep_transcripts:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  default: 0
  type: program_argument
sv_rankvariant:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ranked_
  type: program
sv_genmod_annotate_regions:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_models_family_type:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: mip
  type: program_argument
sv_genmod_models_reduced_penetrance_file:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_genmod_models_whole_gene:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: 0
  type: program_argument
sv_rank_model_file:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
##Sv_reformat
sv_reformat:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  program_name_path:
   - grep
  type: program
sv_rankvariant_binary_file:
  associated_program:
   - sv_reformat
  data_type: SCALAR
  default: 0
  type: program_argument
sv_reformat_remove_genes_file:
  associated_program:
   - sv_reformat
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
##Bcftools
bcftools_mpileup:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _mpileup_
  outdir_name: bcftools
  program_name_path:
   - bcftools
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
bcftools_mpileup_filter_variant:
  associated_program:
   - bcftools_mpileup
  data_type: SCALAR
  default: 0
  type: program_argument
##Freebayes
freebayes:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _freebayes_
  program_name_path:
   - freebayes
   - bcftools
  outdir_name: freebayes
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
## GATK Genotype
gatk_haplotypecaller:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _haptc
  outfile_suffix: ".g.vcf"
  program_name_path:
   - gatk
  type: program
gatk_haplotypecaller_annotation:
  associated_program:
   - gatk_haplotypecaller
  element_separator: ,
  data_type: ARRAY
  default:
   - BaseQualityRankSumTest
   - ChromosomeCounts
   - Coverage
   - DepthPerAlleleBySample
   - FisherStrand
   - MappingQualityRankSumTest
   - QualByDepth
   - RMSMappingQuality
   - ReadPosRankSumTest
   - StrandOddsRatio
  type: program_argument
#BaseQualityRankSumTest;  #Rank Sum Test of REF versus ALT base quality scores
#ChromosomeCounts;  #Counts and frequency of alleles in called genotypes
#Coverage;  #Total depth of coverage per sample and over all samples
#DepthPerAlleleBySample;  #Depth of coverage of each allele per sample
#FisherStrand;  #Strand bias estimated using Fisher's Exact Test
#MappingQualityRankSumTest;  #Rank Sum Test for mapping qualities of REF versus ALT reads
#QualByDepth;  #Variant confidence normalized by unfiltered depth of variant samples
#RMSMappingQuality;  #Root Mean Square of the mapping quality of reads across all samples
#ReadPosRankSumTest;  #Rank Sum Test for relative positioning of REF versus ALT alleles within reads
#StrandOddsRatio ;  #Strand bias estimated by the Symmetric Odds Ratio test
gatk_haplotypecaller_no_soft_clipped_bases:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_haplotypecaller_pcr_indel_model:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: NONE
  type: program_argument
gatk_haplotypecaller_snp_known_set:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: GRCh37_dbsnp_-138-.vcf
  exists_check: file
  reference: reference_dir
  type: path
## GATK Genotype Calibration
gatk_genotypegvcfs:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _gent_
  outfile_suffix: ".vcf"
  program_name_path:
   - gatk
  type: program
gatk_genotypegvcfs_ref_gvcf:
  associated_program:
   - gatk_genotypegvcfs
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
gatk_gathervcfs:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - gatk
  type: program
gatk_gathervcfs_bcf_file:
  associated_program:
   - gatk_gathervcfs
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: vrecal_
  program_name_path:
   - bcftools
   - gatk
  outdir_name: gatk
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
gatk_calculategenotypeposteriors_support_set:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: GRCh37_1000g_sites_-phase3_v4_2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_annotations:
  associated_program:
   - gatk_variantrecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - QD
   - MQRankSum
   - ReadPosRankSum
   - FS
   - SOR
   - DP
  type: program_argument
gatk_variantrecalibration_dp_annotation:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_indel_max_gaussians:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_indel_tsfilter_level:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 99.9
  type: program_argument
gatk_variantrecalibration_resource_indel:
  associated_program:
   - gatk_variantrecalibration
  data_type: HASH
  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"
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_resource_snv:
  associated_program:
   - gatk_variantrecalibration
  data_type: HASH
  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"
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_snv_max_gaussians:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_snv_tsfilter_level:<commit_msg>Fix to VariantRecalibrator resource string, #306<commit_after>---
## Version: 2.1.0
decompose_normalize_references:
  associated_program:
   - mip
  data_type: ARRAY
  default:
   - gatk_baserecalibration_known_sites
   - gatk_haplotypecaller_snp_known_set
   - gatk_variantrecalibration_resource_indel
   - frequency_genmod_filter_1000g
   - sv_vcfanno_config_file
   - gatk_varianteval_gold
   - gatk_varianteval_dbsnp
   - snpsift_annotation_files
  element_separator: ,
  type: mip
exome_target_bed:
  associated_program:
   - picardtools_collecthsmetrics
   - gatk_baserecalibration
   - gatk_haplotypecaller
  build_file: 1
  data_type: HASH
  exists_check: file
  reference: reference_dir
  type: path
expected_coverage:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
## genomeAnalysisToolKitPath
## GATK FTP Bundle Download version. Needed for all programs that download the human genome reference
gatk_bundle_download_version:
  associated_program:
   - bwa_mem
   - gatk_baserecalibration
   - cnvnator
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs 
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  data_type: SCALAR
  default: 2.8
  type: program_argument
gatk_downsample_to_coverage:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 1000
  type: program_argument
gatk_logging_level:
  associated_program:
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - cnvnator
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - rankvariant
  data_type: SCALAR
  default: INFO
  type: program_argument
gatk_path:
  associated_program:
   - bcftools_mpileup
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - rankvariant
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
genomic_set:
  associated_program:
   - mip
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## HumanGenomeReference
human_genome_reference:
  associated_program:
   - mip
   - bwa_mem
   - expansionhunter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - bcftools_mpileup
   - freebayes
   - manta
   - delly_call
   - cnvnator
   - tiddit
   - gatk_variantrecalibration
   - vt
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  data_type: SCALAR
  default: GRCh37_homo_sapiens_-d5-.fasta
  exists_check: file
  reference: reference_dir
  type: path
human_genome_reference_file_endings:
  associated_program:
   - bwa_mem
   - expansionhunter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - bcftools_mpileup
   - freebayes
   - manta
   - delly_call
   - cnvnator
   - tiddit
   - gatk_variantrecalibration
   - vt
   - gatk_variantevalall
   - gatk_variantevalexome
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
  build_file: 1
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## java large pages - affects all modules using java
java_use_large_pages:
  associated_program:
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_genotypegvcfs
   - gatk_gathervcfs
   - gatk_variantrecalibration
   - gatk_combinevariantcallsets
   - gatk_variantevalall
   - gatk_variantevalexome
   - varianteffectpredictor
   - snpeff
  data_type: SCALAR
  default: 0
  type: program_argument
####Bash
module_core_number:
  associated_program:
   - mip
  data_type: HASH
  default:
    analysisrunstatus: 1
    bcftools_mpileup: 16
    bedtools_genomecov: 1
    bwa_mem: 16
    chanjo_sexcheck: 1
    cnvnator: 16
    delly_call: 16
    delly_reformat: 16
    endvariantannotationblock: 1
    evaluation: 1
    expansionhunter: 1
    fastqc: 0
    freebayes: 16
    frequency_filter: 16
    gatk_baserecalibration: 16
    gatk_combinevariantcallsets: 1
    gatk_genotypegvcfs: 2
    gatk_gathervcfs: 2
    gatk_haplotypecaller: 16
    gatk_variantevalall: 1
    gatk_variantevalexome: 1
    gatk_variantrecalibration: 2
    gzip_fastq: 0
    manta: 16
    markduplicates: 16
    multiqc: 1
    peddy: 4
    picardtools_collecthsmetrics: 2
    picardtools_collectmultiplemetrics: 2
    picardtools_mergesamfiles: 16
    plink: 1
    qccollect: 1
    rcovplots: 1
    rtg_vcfeval: 1
    sacct: 1
    sambamba_depth: 2
    samtools_subsample_mt: 1
    split_fastq_file: 4
    sv_annotate: 1
    sv_combinevariantcallsets: 1
    sv_rankvariant: 16
    sv_reformat: 1
    sv_varianteffectpredictor: 16
    sv_vcfparser: 16
    variant_integrity: 1
    vcf2cytosure: 1
  type: mip
module_time:
  associated_program:
   - mip
  data_type: HASH
  default:
    analysisrunstatus: 1
    bwa_mem: 30
    bcftools_mpileup: 40
    bedtools_genomecov: 15
    chanjo_sexcheck: 2
    cnvnator: 5
    delly_call: 10
    delly_reformat: 7
    endvariantannotationblock: 2
    evaluation: 1
    expansionhunter: 1
    fastqc: 10
    freebayes: 20
    frequency_filter: 2
    gatk_baserecalibration: 20
    gatk_combinevariantcallsets: 2
    gatk_genotypegvcfs: 10
    gatk_gathervcfs: 2
    gatk_haplotypecaller: 30
    gatk_variantevalall: 2
    gatk_variantevalexome: 2
    gatk_variantrecalibration: 10
    gzip_fastq: 2
    manta: 10
    markduplicates: 20
    multiqc: 1
    peddy: 1
    picardtools_collecthsmetrics: 10
    picardtools_collectmultiplemetrics: 10
    picardtools_mergesamfiles: 20
    plink: 1
    prepareforvariantannotationblock: 5
    qccollect: 1
    rankvariant: 10
    rcovplots: 1
    rhocall: 5
    rtg_vcfeval: 1
    sacct: 1
    sambamba_depth: 10
    samtools_subsample_mt: 1
    split_fastq_file: 10
    snpeff: 10
    sv_annotate: 2
    sv_combinevariantcallsets: 2
    sv_rankvariant: 2
    sv_reformat: 1
    sv_varianteffectpredictor: 10
    sv_vcfparser: 2
    tiddit: 10
    varianteffectpredictor: 10
    variant_integrity: 1
    vcfparser: 5
    vt: 10
    vcf2cytosure: 10
  type: mip
infile_dirs:
  associated_program:
   - mip
  exists_check: directory
  data_type: HASH
  type: path
  update_path: absolute_path
## Choosen MIP Aligner
outaligner_dir:
  associated_program:
   - mip
  data_type: SCALAR
  mandatory: no
  type: mip
picardtools_path:
  associated_program:
   - bwa_mem
   - picardtools_mergesamfiles
   - markduplicates
   - picardtools_collecthsmetrics
   - picardtools_collectmultiplemetrics
   - prepareforvariantannotationblock
   - delly_reformat
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
reduce_io:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  type: mip
replace_iupac:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  type: mip
###Programs
split_fastq_file:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  outfile_suffix: ".fastq.gz"
  program_name_path:
   - pigz
   - split
  type: program
split_fastq_file_read_batch:
  associated_program:
   - split_fastq_file
  data_type: SCALAR
  default: 25000000
  type: program_argument
## Gzip
gzip_fastq:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 1
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  program_name_path:
   - gzip
  type: program
## FastQC
fastqc:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  infile_suffix: ".fastq"
  program_name_path:
   - fastqc
  type: program
## BWA
bwa_mem:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _sorted
  outfile_suffix: ".bam"
  outdir_name: bwa
  program_name_path:
   - bwa
   - samtools
   - sambamba
  program_type: aligners
  type: program
bwa_build_reference:
  associated_program:
   - bwa_mem
  build_file: 1
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
bwa_mem_bamstats:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 1
  type: program_argument
bwa_mem_cram:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 0
  type: program_argument
bwa_mem_hla:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 0
  type: program_argument
bwa_sambamba_sort_memory_limit:
  associated_program:
   - bwa_mem
  data_type: SCALAR
  default: 32G
  type: program_argument
## BAMCalibrationBlock
bamcalibrationblock:
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  reduce_io: 1
  type: program
picardtools_mergesamfiles:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  type: program
markduplicates:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _md
  program_name_path:
   - sambamba
  type: program
markduplicates_picardtools_markduplicates:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 0
  type: program_argument
markduplicates_sambamba_markdup:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 0
  type: program_argument
markduplicates_sambamba_markdup_hash_table_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 262144
  type: program_argument
markduplicates_sambamba_markdup_io_buffer_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 2048
  type: program_argument
markduplicates_sambamba_markdup_overflow_list_size:
  associated_program:
   - markduplicates
  data_type: SCALAR
  default: 200000
  type: program_argument
## GATK BAM Calibration
gatk_baserecalibration:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _brecal
  program_name_path:
   - gatk
  type: program
gatk_baserecalibration_known_sites:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - GRCh37_dbsnp_-138-.vcf
   - GRCh37_1000g_indels_-phase1-.vcf
   - GRCh37_mills_and_1000g_indels_-gold_standard-.vcf
  exists_check: file
  reference: reference_dir
  type: path
gatk_baserecalibration_read_filters:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - OverclippedReadFilter
  type: program_argument
gatk_baserecalibration_static_quantized_quals:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  default:
   - 10
   - 20
   - 30
   - 40
  type: program_argument
## Coverage Analysis
chanjo_sexcheck:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _sex
  outfile_suffix: ".tsv"
  program_name_path:
   - chanjo
  type: program
chanjo_sexcheck_log_level:
  associated_program:
   - chanjo_sexcheck
  data_type: SCALAR
  default: DEBUG
  type: program_argument
samtools_subsample_mt:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _subsample_MT
  outfile_suffix: ".bam"
  program_name_path: 
   - samtools
  type: program
samtools_subsample_mt_depth:
  analysis_mode: sample
  associated_program:
   - samtools_subsample_mt
  data_type: SCALAR
  default: 60
  type: program_argument
sambamba_depth:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _coverage
  outfile_suffix: ".bed"
  program_name_path:
   - sambamba
  type: program
sambamba_depth_base_quality:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 10
  type: program_argument
sambamba_depth_bed:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sambamba_depth_cutoffs:
  associated_program:
   - sambamba_depth
  element_separator: ,
  data_type: ARRAY
  default:
   - 10
   - 15
   - 20
   - 50
   - 100
  type: program_argument
sambamba_depth_mode:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: region
  type: program_argument
sambamba_depth_noduplicates:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 0
  type: program_argument
sambamba_depth_mapping_quality:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 10
  type: program_argument
sambamba_depth_quality_control:
  associated_program:
   - sambamba_depth
  data_type: SCALAR
  default: 1
  type: program_argument
bedtools_genomecov:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _genomecov
  program_name_path:
   - bedtools
  type: program
bedtools_genomecov_max_coverage:
  associated_program:
   - bedtools_genomecov
  data_type: SCALAR
  default: 30
  type: program_argument
picardtools_collectmultiplemetrics:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  type: program
picardtools_collecthsmetrics:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _collecthsmetrics
  type: program
rcovplots:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: nofile_tag
  type: program
## Structural Variant Calling
cnvnator:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _cnvnator
  outdir_name: cnvnator
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - cnvnator
   - samtools
  program_type: structural_variant_callers
  type: program
cnv_bin_size:
  associated_program:
   - cnvnator
  data_type: SCALAR
  default: 1000
  type: program_argument
delly_call:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _dellycall
  program_name_path:
   - delly
  outdir_name: delly
  outfile_suffix: ".bcf"
  type: program
delly_reformat:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _dellyreformat
  program_name_path:
   - delly
   - bcftools
  outdir_name: delly
  outfile_suffix: ".vcf"
  program_type: structural_variant_callers
  type: program
delly_exclude_file:
  associated_program:
   - delly_call
   - delly_reformat
  data_type: SCALAR
  default: hg19_human_excl_-0.7.6-.tsv
  exists_check: file
  reference: reference_dir
  type: path
delly_types:
  associated_program:
   - delly_call
   - delly_reformat
  element_separator: ,
  data_type: ARRAY
  default:
   - DEL
   - DUP
   - INV
   - INS
  type: program_argument
expansionhunter:
  analysis_mode: sample
  associated_program:  
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _exphun
  outdir_name: expansionhunter
  outfile_suffix: ".vcf"
  program_name_path:
   - ExpansionHunter
  program_type: structural_variant_callers
  type: program
expansionhunter_repeat_specs_dir:
  associated_program:
   - expansionhunter
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
manta:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _manta
  program_name_path:
   - configManta.py
  outdir_name: manta
  outfile_suffix: ".vcf"
  program_type: structural_variant_callers
  type: program
tiddit:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _tiddit
  outdir_name: tiddit
  outfile_suffix: ".vcf"
  coverage_file_suffix: ".tab"
  program_name_path:
   - TIDDIT.py
  program_type: structural_variant_callers
  type: program
tiddit_bin_size:
  associated_program:
   - vcf2cytosure
   - tiddit
  data_type: SCALAR
  default: 500
  type: program_argument
tiddit_minimum_number_supporting_pairs:
  associated_program:
   - tiddit
  data_type: SCALAR
  default: 6
  type: program_argument
sv_combinevariantcallsets:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _comb_
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - svdb
   - vt
  type: program
sv_combinevariantcallsets_bcf_file:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  default: 0
  type: program_argument
sv_svdb_merge_prioritize:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  mandatory: no
  type: program_argument
sv_vt_decompose:
  associated_program:
   - sv_combinevariantcallsets
  data_type: SCALAR
  default: 0
  type: program_argument
sv_annotate:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ann_
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - svdb
  type: program
sv_bcftools_view_filter:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_filter:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_filter_threshold:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0.10
  type: program_argument
sv_genmod_filter_1000g:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: GRCh37_all_wgs_-phase3_v5b.2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
sv_svdb_query:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_svdb_query_db_files:
  associated_program:
   - sv_annotate
  data_type: HASH
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: 0
  type: program_argument
sv_vcfannotation_header_lines_file:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno_config:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_vcfanno_config_file:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  default: GRCh37_all_sv_-phase3_v2.2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
  type: program_argument
sv_vcfanno_lua:
  associated_program:
   - sv_annotate
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
vcf2cytosure:
  analysis_mode: family
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: cyto_
  outfile_suffix: ".cgh"
  outdir_name: vcf2cytosure
  program_name_path:
    - TIDDIT.py
    - vcf2cytosure
    - bcftools
  type: program
vcf2cytosure_exclude_filter:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: ""
  type: program_argument
vcf2cytosure_freq:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0.01
  type: program_argument
vcf2cytosure_freq_tag:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: FRQ
  type: program_argument
vf2cytosure_no_filter:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0
  type: program_argument
vcf2cytosure_var_size:
  associated_program:
   - vcf2cytosure
  data_type: SCALAR
  default: 0
  type: program_argument
sv_varianteffectpredictor:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: vep_
  program_name_path:
   - vep
  type: program
sv_vep_features:
  associated_program:
   - sv_varianteffectpredictor
  element_separator: ,
  data_type: ARRAY
  default:
   - hgvs
   - symbol
   - numbers
   - humdiv
   - domains
   - protein
   - ccds
   - uniprot
   - biotype
   - regulatory
   - tsl
   - canonical
   - per_gene
   - appris
   - cache
   - force_overwrite
   - no_progress
   - offline
  type: program_argument
sv_vep_plugins:
  associated_program:
   - sv_varianteffectpredictor
  element_separator: ,
  data_type: ARRAY
  default:
   - LoFtool
  type: program_argument
sv_vcfparser:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: parsed_
  type: program
sv_vcfparser_range_feature_annotation_columns:
  associated_program:
   - sv_vcfparser
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  type: program_argument
sv_vcfparser_range_feature_file:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
sv_vcfparser_outfile_count:
  associated_program:
   - sv_vcfparser
   - mip
  data_type: SCALAR
  default: 1
  type: program_argument
sv_vcfparser_per_gene:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  default: 0
  type: program_argument
sv_vcfparser_select_feature_annotation_columns:
  associated_program:
   - sv_vcfparser
  element_separator: ,
  data_type: ARRAY
  mandatory: no
  type: program_argument
sv_vcfparser_select_file:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  exists_check: file
  type: path
  update_path: absolute_path
sv_vcfparser_select_file_matching_column:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  type: program_argument
sv_vcfparser_vep_transcripts:
  associated_program:
   - sv_vcfparser
  data_type: SCALAR
  default: 0
  type: program_argument
sv_rankvariant:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ranked_
  type: program
sv_genmod_annotate_regions:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: 0
  type: program_argument
sv_genmod_models_family_type:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: mip
  type: program_argument
sv_genmod_models_reduced_penetrance_file:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
sv_genmod_models_whole_gene:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  default: 0
  type: program_argument
sv_rank_model_file:
  associated_program:
   - sv_rankvariant
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
##Sv_reformat
sv_reformat:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  program_name_path:
   - grep
  type: program
sv_rankvariant_binary_file:
  associated_program:
   - sv_reformat
  data_type: SCALAR
  default: 0
  type: program_argument
sv_reformat_remove_genes_file:
  associated_program:
   - sv_reformat
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
##Bcftools
bcftools_mpileup:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _mpileup_
  outdir_name: bcftools
  program_name_path:
   - bcftools
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
bcftools_mpileup_filter_variant:
  associated_program:
   - bcftools_mpileup
  data_type: SCALAR
  default: 0
  type: program_argument
##Freebayes
freebayes:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _freebayes_
  program_name_path:
   - freebayes
   - bcftools
  outdir_name: freebayes
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
## GATK Genotype
gatk_haplotypecaller:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _haptc
  outfile_suffix: ".g.vcf"
  program_name_path:
   - gatk
  type: program
gatk_haplotypecaller_annotation:
  associated_program:
   - gatk_haplotypecaller
  element_separator: ,
  data_type: ARRAY
  default:
   - BaseQualityRankSumTest
   - ChromosomeCounts
   - Coverage
   - DepthPerAlleleBySample
   - FisherStrand
   - MappingQualityRankSumTest
   - QualByDepth
   - RMSMappingQuality
   - ReadPosRankSumTest
   - StrandOddsRatio
  type: program_argument
#BaseQualityRankSumTest;  #Rank Sum Test of REF versus ALT base quality scores
#ChromosomeCounts;  #Counts and frequency of alleles in called genotypes
#Coverage;  #Total depth of coverage per sample and over all samples
#DepthPerAlleleBySample;  #Depth of coverage of each allele per sample
#FisherStrand;  #Strand bias estimated using Fisher's Exact Test
#MappingQualityRankSumTest;  #Rank Sum Test for mapping qualities of REF versus ALT reads
#QualByDepth;  #Variant confidence normalized by unfiltered depth of variant samples
#RMSMappingQuality;  #Root Mean Square of the mapping quality of reads across all samples
#ReadPosRankSumTest;  #Rank Sum Test for relative positioning of REF versus ALT alleles within reads
#StrandOddsRatio ;  #Strand bias estimated by the Symmetric Odds Ratio test
gatk_haplotypecaller_no_soft_clipped_bases:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_haplotypecaller_pcr_indel_model:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: NONE
  type: program_argument
gatk_haplotypecaller_snp_known_set:
  associated_program:
   - gatk_haplotypecaller
  data_type: SCALAR
  default: GRCh37_dbsnp_-138-.vcf
  exists_check: file
  reference: reference_dir
  type: path
## GATK Genotype Calibration
gatk_genotypegvcfs:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _gent_
  outfile_suffix: ".vcf"
  program_name_path:
   - gatk
  type: program
gatk_genotypegvcfs_ref_gvcf:
  associated_program:
   - gatk_genotypegvcfs
  data_type: SCALAR
  exists_check: file
  reference: reference_dir
  type: path
gatk_gathervcfs:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: ""
  outfile_suffix: ".vcf"
  program_name_path:
   - bcftools
   - gatk
  type: program
gatk_gathervcfs_bcf_file:
  associated_program:
   - gatk_gathervcfs
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration:
  analysis_mode: family
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: vrecal_
  program_name_path:
   - bcftools
   - gatk
  outdir_name: gatk
  program_type: variant_callers
  outfile_suffix: ".vcf"
  type: program
gatk_calculategenotypeposteriors_support_set:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: GRCh37_1000g_sites_-phase3_v4_2013-05-02-.vcf.gz
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_annotations:
  associated_program:
   - gatk_variantrecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - QD
   - MQRankSum
   - ReadPosRankSum
   - FS
   - SOR
   - DP
  type: program_argument
gatk_variantrecalibration_dp_annotation:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_indel_max_gaussians:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_indel_tsfilter_level:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 99.9
  type: program_argument
gatk_variantrecalibration_resource_indel:
  associated_program:
   - gatk_variantrecalibration
  data_type: HASH
  default:
     GRCh37_dbsnp_-138-.vcf: "dbsnp,known=true,training=false,truth=false,prior=2.0"
     GRCh37_mills_and_1000g_indels_-gold_standard-.vcf: "mills,known=true,training=true,truth=true,prior=12.0"
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_resource_snv:
  associated_program:
   - gatk_variantrecalibration
  data_type: HASH
  default:
     GRCh37_dbsnp_-138-.vcf: "dbsnp,known=true,training=false,truth=false,prior=2.0"
     GRCh37_hapmap_-3.3-.vcf: "hapmap,known=false,training=true,truth=true,prior=15.0"
     GRCh37_1000g_omni_-2.5-.vcf: "omni,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"
  exists_check: file
  reference: reference_dir
  type: path
gatk_variantrecalibration_snv_max_gaussians:
  associated_program:
   - gatk_variantrecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_variantrecalibration_snv_tsfilter_level:
{'fraction_non_alphanumeric': 0.05610804174340086, 'fraction_numerical': 0.015346838551258441, 'mean_word_length': 3.9865313975861465, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3003358', 'n_tokens_mistral': 22232, 'n_tokens_neox': 21225, 'n_words': 4184}