example_inputs.yaml

BC_abra2_output_bams: null
BC_bwa_mem_output: null
BC_gatk_merge_bam_alignment_output_file_name: null
BC_gatk_sam_to_fastq_output_name_R1: null
BC_gatk_sam_to_fastq_output_name_R2: null
BC_picard_addRG_output_file_name: null
BC_picard_fixmate_information_output_file_name: null
UBG_abra2_output_bams: null
UBG_bwa_mem_output: null
UBG_gatk_merge_bam_alignment_output_file_name: null
UBG_picard_SamToFastq_R1_output_fastq: null
UBG_picard_SamToFastq_R2_output_fastq: null
UBG_picard_addRG_output_file_name: null
UBG_picard_fixmateinformation_output_file_name: null
abra2_bam_index: null
abra2_consensus_sequence: null
abra2_contig_anchor: null
abra2_maximum_average_depth: null
abra2_maximum_mixmatch_rate: null
abra2_no_edge_complex_indel: null
abra2_scoring_gap_alignments: null
abra2_soft_clip_contig: null
abra2_window_size: null
apply_bqsr_output_file_name: null
base_recalibrator_output_file_name: null
bedtools_genomecov_option_bedgraph: null
bedtools_merge_distance_between_features: null
bwa_mem_K: null
bwa_mem_T: null
bwa_mem_Y: null
create_bam_index: null
fastp_html_output_file_name: null
fastp_json_output_file_name: null
fastp_minimum_read_length: null
fastp_read1_adapter_sequence: null
fastp_read1_output_file_name: null
fastp_read2_adapter_sequence: null
fastp_read2_output_file_name: null
fgbio_async_io: null
fgbio_call_duplex_consensus_reads_min_reads: null
fgbio_call_duplex_consensus_reads_output_file_name: null
fgbio_collect_duplex_seq_metrics_duplex_umi_counts: null
fgbio_collect_duplex_seq_metrics_intervals: null
fgbio_collect_duplex_seq_metrics_output_prefix: null
fgbio_fastq_to_bam_input: null
fgbio_filter_consensus_read_min_base_quality_duplex: null
fgbio_filter_consensus_read_min_base_quality_simplex_duplex: null
fgbio_filter_consensus_read_min_reads_duplex: null
fgbio_filter_consensus_read_min_reads_simplex_duplex: null
fgbio_filter_consensus_read_output_file_name_duplex: null
fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics: null
fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics: null
fgbio_filter_consensus_read_output_file_name_simplex_duplex: null
fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex: null
fgbio_group_reads_by_umi_family_size_histogram: null
fgbio_group_reads_by_umi_output_file_name: null
fgbio_group_reads_by_umi_strategy: null
fgbio_postprocessing_output_file_name_simplex: null
gatk_base_recalibrator_add_output_sam_program_record: null
gatk_base_recalibrator_known_sites:
  - class: File
    metadata: {}
    path: >-
      /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/dbsnp_137_14_16.b37.vcf
    secondaryFiles:
      - class: File
        path: >-
          /Users/shahr2/Documents/test_reference/test_nucleo/known_sites/dbsnp_137_14_16.b37.vcf.idx
  - class: File
    metadata: {}
    path: >-
      /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf
    secondaryFiles:
      - class: File
        path: >-
          /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf.idx
gatk_collect_alignment_summary_metrics_output_file_name: null
gatk_mark_duplicates_duplication_metrics_file_name: null
gatk_mark_duplicates_output_file_name: null
gatk_merge_sam_files_output_file_name: null
library: null
merge_sam_files_sort_order: null
optical_duplicate_pixel_distance: null
picard_addRG_sort_order: null
platform: null
platform-model: null
platform-unit: null
read-group-id: null
read-structures: null
reference_sequence:
  class: File
  metadata: {}
  path: /Users/shahr2/Documents/test_reference/fasta/chr14_chr16.fasta
  secondaryFiles:
    - class: File
      path: ../../test_reference/fasta/chr14_chr16.fasta.amb
    - class: File
      path: ../../test_reference/fasta/chr14_chr16.fasta.ann
run-date: null
sample: null
sequencing-center: null
sort_order: null
temporary_directory: null
validation_stringency: null