cnv_common_tasks

PreprocessIntervals

description
Reusing workflow from GATK Git Repository: https://github.com/broadinstitute/gatk/blob/master/scripts/cnv_wdl/cnv_common_tasks.wdl

Inputs

Required

  • gatk_docker (String, required)
  • ref_fasta (File, required)
  • ref_fasta_dict (File, required)
  • ref_fasta_fai (File, required)

Optional

  • bin_length (Int?)
  • blacklist_intervals (File?)
  • cpu (Int?)
  • disk_space_gb (Int?)
  • gatk4_jar_override (File?)
  • intervals (File?)
  • mem_gb (Int?)
  • padding (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • preprocessed_intervals (File)

AnnotateIntervals

Inputs

Required

  • gatk_docker (String, required)
  • intervals (File, required)
  • ref_fasta (File, required)
  • ref_fasta_dict (File, required)
  • ref_fasta_fai (File, required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • feature_query_lookahead (Int?)
  • gatk4_jar_override (File?)
  • mappability_track_bed (File?)
  • mappability_track_bed_idx (File?)
  • mem_gb (Int?)
  • preemptible_attempts (Int?)
  • segmental_duplication_track_bed (File?)
  • segmental_duplication_track_bed_idx (File?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • annotated_intervals (File)

FilterIntervals

Inputs

Required

  • gatk_docker (String, required)
  • intervals (File, required)

Optional

  • annotated_intervals (File?)
  • blacklist_intervals (File?)
  • cpu (Int?)
  • disk_space_gb (Int?)
  • extreme_count_filter_maximum_percentile (Float?)
  • extreme_count_filter_minimum_percentile (Float?)
  • extreme_count_filter_percentage_of_samples (Float?)
  • gatk4_jar_override (File?)
  • low_count_filter_count_threshold (Int?)
  • low_count_filter_percentage_of_samples (Float?)
  • maximum_gc_content (Float?)
  • maximum_mappability (Float?)
  • maximum_segmental_duplication_content (Float?)
  • mem_gb (Int?)
  • minimum_gc_content (Float?)
  • minimum_mappability (Float?)
  • minimum_segmental_duplication_content (Float?)
  • preemptible_attempts (Int?)
  • read_count_files (Array[File]?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • filtered_intervals (File)

CollectCounts

Inputs

Required

  • bam (File, required)
  • bam_idx (File, required)
  • gatk_docker (String, required)
  • intervals (File, required)
  • ref_fasta (File, required)
  • ref_fasta_dict (File, required)
  • ref_fasta_fai (File, required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • enable_indexing (Boolean?)
  • format (String?)
  • gatk4_jar_override (File?)
  • mem_gb (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • entity_id (String)
  • counts (File)

CollectAllelicCounts

Inputs

Required

  • bam (File, required)
  • bam_idx (File, required)
  • common_sites (File, required)
  • gatk_docker (String, required)
  • ref_fasta (File, required)
  • ref_fasta_dict (File, required)
  • ref_fasta_fai (File, required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • gatk4_jar_override (File?)
  • mem_gb (Int?)
  • minimum_base_quality (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • entity_id (String)
  • allelic_counts (File)

ScatterIntervals

Inputs

Required

  • gatk_docker (String, required)
  • interval_list (File, required)
  • num_intervals_per_scatter (Int, required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • gatk4_jar_override (File?)
  • mem_gb (Int?)
  • output_dir (String?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • scattered_interval_lists (Array[File])

PostprocessGermlineCNVCalls

Inputs

Required

  • calling_configs (Array[File], required)
  • contig_ploidy_calls_tar (File, required)
  • denoising_configs (Array[File], required)
  • entity_id (String, required)
  • gatk_docker (String, required)
  • gcnv_calls_tars (Array[File], required)
  • gcnv_model_tars (Array[File], required)
  • gcnvkernel_version (Array[File], required)
  • ref_copy_number_autosomal_contigs (Int, required)
  • sample_index (Int, required)
  • sharded_interval_lists (Array[File], required)

Optional

  • allosomal_contigs (Array[String]?)
  • cpu (Int?)
  • disk_space_gb (Int?)
  • gatk4_jar_override (File?)
  • mem_gb (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • genotyped_intervals_vcf (File)
  • genotyped_segments_vcf (File)
  • denoised_copy_ratios (File)

CollectSampleQualityMetrics

Inputs

Required

  • entity_id (String, required)
  • gatk_docker (String, required)
  • genotyped_segments_vcf (File, required)
  • maximum_number_events (Int, required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • mem_gb (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • qc_status_file (File)
  • qc_status_string (String)

CollectModelQualityMetrics

Inputs

Required

  • gatk_docker (String, required)
  • gcnv_model_tars (Array[File], required)

Optional

  • cpu (Int?)
  • disk_space_gb (Int?)
  • mem_gb (Int?)
  • preemptible_attempts (Int?)

Defaults

  • use_ssd (Boolean, default=false)

Outputs

  • qc_status_file (File)
  • qc_status_string (String)