<commit_before>---
## Version: 2.1.2
## HumanGenomeReference
human_genome_reference:
  associated_program:
   - mip
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
   - star_aln
  data_type: SCALAR
  default: GRCh37_homo_sapiens_-d5-.fasta
  exists_check: file
  reference: reference_dir
  type: path
human_genome_reference_file_endings:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
   - star_aln
  build_file: 1
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## GATK FTP Bundle Download version. Needed for all programs that download the human genome reference
gatk_bundle_download_version:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 2.8
  type: program_argument
gatk_disable_auto_index_and_file_lock:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_downsample_to_coverage:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 1000
  type: program_argument
gatk_logging_level:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  default: INFO
  type: program_argument
gatk_path:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
infile_dirs:
  associated_program:
   - mip
  exists_check: directory
  data_type: HASH
  type: path
  update_path: absolute_path
## java large pages - affects all modules using java
java_use_large_pages:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_variantfiltration
   - star_aln
  data_type: SCALAR
  default: 0
  type: program_argument
####Bash
module_time:
  associated_program:
   - mip
  data_type: HASH
  default:
    bootstrapann: 3
    fastqc: 1
    gatk_asereadcounter: 2
    gatk_baserecalibration: 5
    gatk_haplotypecaller: 2
    gatk_splitncigarreads: 1
    gatk_variantfiltration: 1
    gzip_fastq: 2
    markduplicates: 4
    picardtools_mergesamfiles: 2
    salmon_quant: 5
    star_aln: 5
    star_fusion: 1
  type: mip
module_core_number:
  associated_program:
   - mip
  data_type: HASH
  default:
    bootstrapann: 1
    fastqc: 0
    gatk_asereadcounter: 1
    gatk_baserecalibration: 16
    gatk_haplotypecaller: 16
    gatk_splitncigarreads: 16
    gatk_variantfiltration: 1
    gzip_fastq: 0
    markduplicates: 16
    picardtools_mergesamfiles: 16
    salmon_quant: 1
    star_aln: 16
    star_fusion: 1
  type: mip
## Choosen MIP Aligner
outaligner_dir:
  associated_program:
   - mip
  data_type: SCALAR
  mandatory: no
  type: mip
picardtools_path:
  associated_program:
   - markduplicates
   - picardtools_mergesamfiles
   - star_aln
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
sample_origin:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
time_point:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
###Programs
## 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
## Salmon
salmon_quant:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _salmon
  outfile_suffix: ".sf"
  outdir_name: salmon
  program_name_path:
   - salmon
  type: program
salmon_rna_lib_configuration:
  associated_program:
   - salmon_quant
  data_type: SCALAR
  default: ISF
  type: program_argument
## Star Aln
star_aln:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _star_sorted
  outfile_suffix: ".bam"
  outdir_name: star
  program_name_path:
   - STAR
  program_type: aligners
  type: program
align_intron_max:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 100000
  type: program_argument
align_mates_gap_max:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 100000
  type: program_argument
align_sjdb_overhang_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 10
  type: program_argument
chim_junction_overhang_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 12
  type: program_argument
chim_segment_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 12
  type: program_argument
star_aln_reference_genome:
  associated_program:
   - star_aln
  build_file: 1
  data_type: SCALAR
  exists_check: directory
  mandatory: no
  reference: reference_dir
  type: path
star_aln_transcripts_file:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: GRCh37_transcripts_-v1_0-.GTF 
  exists_check: file
  reference: reference_dir
  type: path
two_pass_mode:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: Basic
  type: program_argument
## Star Fusion
star_fusion:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _fusion
  outfile_suffix: ".tsv"
  outdir_name: star
  program_name_path:
    - STAR-Fusion
    - gtf_file_to_feature_seqs.pl
    - prep_genome_lib.pl
  type: program
fusion_filter_reference_genome:
  associated_program:
   - star_fusion
  build_file: 1
  data_type: SCALAR
  exists_check: directory
  mandatory: no
  reference: reference_dir
  type: path
fusion_filter_transcripts_file:
  associated_program:
   - star_fusion
  data_type: SCALAR
  default: GRCh37_transcripts_-v1_0-.GTF
  exists_check: file
  reference: reference_dir
  type: path
## Merge bam files
picardtools_mergesamfiles:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _merged
  type: program
## Mark duplicates
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 SplitNCigarReads
gatk_splitncigarreads:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _splitcigar
  type: program
## GATK BAM Calibration
gatk_baserecalibration:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _brecal
  type: program
gatk_baserecalibration_covariates:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - ContextCovariate
   - CycleCovariate
   - QualityScoreCovariate
   - ReadGroupCovariate
  type: program_argument
gatk_baserecalibration_disable_indel_qual:
  associated_program:
   - gatk_baserecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_baserecalibration_known_sites:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - GRCh37_1000g_indels_-phase1-.vcf
   - GRCh37_dbsnp_-138-.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:
   - OverclippedRead
  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
## GATK Genotype
gatk_haplotypecaller:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _haptc
  outfile_suffix: ".vcf"
  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: CONSERVATIVE
  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 ASE
gatk_asereadcounter:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _ase
  outfile_suffix: ".csv"
  type: program
## GATK VariantFiltration
gatk_variantfiltration:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _filtered
  outfile_suffix: ".vcf"
  type: program
gatk_variantfiltration_cluster_size:
  associated_program:
    - gatk_variantfiltration
  data_type: SCALAR
  default: 3
  type: program_argument
gatk_variantfiltration_filter:
  associated_program:
    - gatk_variantfiltration
  data_type: HASH
  default:
    FS: "FS > 30.0"
    QD: "QD < 2.0"
  type: program_argument
gatk_variantfiltration_cluster_window_size:
  associated_program:
    - gatk_variantfiltration
  data_type: SCALAR
  default: 35
  type: program_argument
## BootstrapAnn
bootstrapann:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _bootstr
  outfile_suffix: ".vcf"
  type: program
<commit_msg>Added more bin deps for star-fusion<commit_after>---
## Version: 2.1.2
## HumanGenomeReference
human_genome_reference:
  associated_program:
   - mip
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
   - star_aln
  data_type: SCALAR
  default: GRCh37_homo_sapiens_-d5-.fasta
  exists_check: file
  reference: reference_dir
  type: path
human_genome_reference_file_endings:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
   - star_aln
  build_file: 1
  data_type: SCALAR
  exists_check: file
  mandatory: no
  reference: reference_dir
  type: path
## GATK FTP Bundle Download version. Needed for all programs that download the human genome reference
gatk_bundle_download_version:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 2.8
  type: program_argument
gatk_disable_auto_index_and_file_lock:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_downsample_to_coverage:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
  data_type: SCALAR
  default: 1000
  type: program_argument
gatk_logging_level:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  default: INFO
  type: program_argument
gatk_path:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_splitncigarreads
   - gatk_variantfiltration
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
infile_dirs:
  associated_program:
   - mip
  exists_check: directory
  data_type: HASH
  type: path
  update_path: absolute_path
## java large pages - affects all modules using java
java_use_large_pages:
  associated_program:
   - gatk_asereadcounter
   - gatk_baserecalibration
   - gatk_haplotypecaller
   - gatk_variantfiltration
   - star_aln
  data_type: SCALAR
  default: 0
  type: program_argument
####Bash
module_time:
  associated_program:
   - mip
  data_type: HASH
  default:
    bootstrapann: 3
    fastqc: 1
    gatk_asereadcounter: 2
    gatk_baserecalibration: 5
    gatk_haplotypecaller: 2
    gatk_splitncigarreads: 1
    gatk_variantfiltration: 1
    gzip_fastq: 2
    markduplicates: 4
    picardtools_mergesamfiles: 2
    salmon_quant: 5
    star_aln: 5
    star_fusion: 1
  type: mip
module_core_number:
  associated_program:
   - mip
  data_type: HASH
  default:
    bootstrapann: 1
    fastqc: 0
    gatk_asereadcounter: 1
    gatk_baserecalibration: 16
    gatk_haplotypecaller: 16
    gatk_splitncigarreads: 16
    gatk_variantfiltration: 1
    gzip_fastq: 0
    markduplicates: 16
    picardtools_mergesamfiles: 16
    salmon_quant: 1
    star_aln: 16
    star_fusion: 1
  type: mip
## Choosen MIP Aligner
outaligner_dir:
  associated_program:
   - mip
  data_type: SCALAR
  mandatory: no
  type: mip
picardtools_path:
  associated_program:
   - markduplicates
   - picardtools_mergesamfiles
   - star_aln
  data_type: SCALAR
  exists_check: directory
  type: path
  update_path: absolute_path
sample_origin:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
time_point:
  associated_program:
   - mip
  data_type: HASH
  mandatory: no
  type: mip
###Programs
## 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
## Salmon
salmon_quant:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _salmon
  outfile_suffix: ".sf"
  outdir_name: salmon
  program_name_path:
   - salmon
  type: program
salmon_rna_lib_configuration:
  associated_program:
   - salmon_quant
  data_type: SCALAR
  default: ISF
  type: program_argument
## Star Aln
star_aln:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _star_sorted
  outfile_suffix: ".bam"
  outdir_name: star
  program_name_path:
   - STAR
  program_type: aligners
  type: program
align_intron_max:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 100000
  type: program_argument
align_mates_gap_max:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 100000
  type: program_argument
align_sjdb_overhang_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 10
  type: program_argument
chim_junction_overhang_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 12
  type: program_argument
chim_segment_min:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: 12
  type: program_argument
star_aln_reference_genome:
  associated_program:
   - star_aln
  build_file: 1
  data_type: SCALAR
  exists_check: directory
  mandatory: no
  reference: reference_dir
  type: path
star_aln_transcripts_file:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: GRCh37_transcripts_-v1_0-.GTF 
  exists_check: file
  reference: reference_dir
  type: path
two_pass_mode:
  associated_program:
   - star_aln
  data_type: SCALAR
  default: Basic
  type: program_argument
## Star Fusion
star_fusion:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _fusion
  outfile_suffix: ".tsv"
  outdir_name: star
  program_name_path:
    - gtf_file_to_feature_seqs.pl
    - prep_genome_lib.pl
    - samtools
    - STAR
    - STAR-Fusion
  type: program
fusion_filter_reference_genome:
  associated_program:
   - star_fusion
  build_file: 1
  data_type: SCALAR
  exists_check: directory
  mandatory: no
  reference: reference_dir
  type: path
fusion_filter_transcripts_file:
  associated_program:
   - star_fusion
  data_type: SCALAR
  default: GRCh37_transcripts_-v1_0-.GTF
  exists_check: file
  reference: reference_dir
  type: path
## Merge bam files
picardtools_mergesamfiles:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _merged
  type: program
## Mark duplicates
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 SplitNCigarReads
gatk_splitncigarreads:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _splitcigar
  type: program
## GATK BAM Calibration
gatk_baserecalibration:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _brecal
  type: program
gatk_baserecalibration_covariates:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - ContextCovariate
   - CycleCovariate
   - QualityScoreCovariate
   - ReadGroupCovariate
  type: program_argument
gatk_baserecalibration_disable_indel_qual:
  associated_program:
   - gatk_baserecalibration
  data_type: SCALAR
  default: 0
  type: program_argument
gatk_baserecalibration_known_sites:
  associated_program:
   - gatk_baserecalibration
  element_separator: ,
  data_type: ARRAY
  default:
   - GRCh37_1000g_indels_-phase1-.vcf
   - GRCh37_dbsnp_-138-.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:
   - OverclippedRead
  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
## GATK Genotype
gatk_haplotypecaller:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _haptc
  outfile_suffix: ".vcf"
  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: CONSERVATIVE
  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 ASE
gatk_asereadcounter:
  analysis_mode: sample
  associated_program:
   - mip
  data_type: SCALAR
  default: 0
  file_tag: _ase
  outfile_suffix: ".csv"
  type: program
## GATK VariantFiltration
gatk_variantfiltration:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _filtered
  outfile_suffix: ".vcf"
  type: program
gatk_variantfiltration_cluster_size:
  associated_program:
    - gatk_variantfiltration
  data_type: SCALAR
  default: 3
  type: program_argument
gatk_variantfiltration_filter:
  associated_program:
    - gatk_variantfiltration
  data_type: HASH
  default:
    FS: "FS > 30.0"
    QD: "QD < 2.0"
  type: program_argument
gatk_variantfiltration_cluster_window_size:
  associated_program:
    - gatk_variantfiltration
  data_type: SCALAR
  default: 35
  type: program_argument
## BootstrapAnn
bootstrapann:
  analysis_mode: sample
  associated_program:
    - mip
  data_type: SCALAR
  default: 0
  file_tag: _bootstr
  outfile_suffix: ".vcf"
  type: program

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