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DNASeqStructs.wdl
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DNASeqStructs.wdl
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version 1.0
struct SampleAndUnmappedBams {
String base_file_name
String? final_gvcf_base_name
Array[File] flowcell_unmapped_bams
String sample_name
String unmapped_bam_suffix
}
struct ReferenceFasta {
File ref_dict
File ref_fasta
File ref_fasta_index
File ref_alt
File ref_sa
File ref_amb
File ref_bwt
File ref_ann
File ref_pac
File? ref_str
}
struct DragmapReference {
File reference_bin
File hash_table_cfg_bin
File hash_table_cmp
}
struct DNASeqSingleSampleReferences {
File contamination_sites_ud
File contamination_sites_bed
File contamination_sites_mu
File calling_interval_list
ReferenceFasta reference_fasta
Array[File] known_indels_sites_vcfs
Array[File] known_indels_sites_indices
File dbsnp_vcf
File dbsnp_vcf_index
File evaluation_interval_list
File haplotype_database_file
}
struct VariantCallingScatterSettings {
Int haplotype_scatter_count
Int break_bands_at_multiples_of
}
struct ExomeGermlineSingleSampleOligos {
File target_interval_list
File bait_interval_list
String bait_set_name
}
struct CrossSpeciesContaminationReferences {
File filter_bwa_image
File kmer_file
File meats_bwa_image
File meats_fasta
File meats_fasta_dict
File meats_taxonomy_file
File microbe_bwa_image
File microbe_fasta
File microbe_fasta_dict
File microbe_taxonomy_file
File normalization_file
File metrics_script_file
Float score_min_identity
Int reads_after_downsampling
}
struct PapiSettings {
Int preemptible_tries
Int agg_preemptible_tries
}