Inputs Description

Input files and parameters required to run workflow

Common workflow language execution engines accept two types of input that are JSON or YAML, please make sure to use one of these while generating the input file. For more information refer to: http://www.commonwl.org/user_guide/yaml/

Parameter Used by Tools

Common Parameters Across Tools

Argument Name	Summary	Default Value
uncollapsed_bam	Base-recalibrated uncollapsed BAM file.(Required)
collapsed_bam	Collapsed BAM file.(Required)
group_reads_by_umi_bam	Collapsed BAM file produced by fgbio's GroupReadsByUmi tool.(Required)
duplex_bam	Duplex BAM file.(Required)
simplex_bam	Simplex BAM file.(Required)
sample_name	The sample name (Required)
sample_group	The sample group (e.g. the patient ID).
sample_sex	The sample sex (e.g. M). (Required)
pool_a_bait_intervals	The Pool A bait interval file.(Required)
pool_a_target_intervals	The Pool A targets interval file.(Required)
pool_b_bait_intervals	The Pool B bait interval file.(Required)
pool_b_target_intervals	The Pool B targets interval file.(Required)
noise_sites_bed	BED file containing sites for duplex noise calculation.(Required)
biometrics_vcf_file	VCF file containing sites for genotyping and contamination calculations.(Required)
reference	Reference sequence file. Please include ".fai", "^.dict", ".amb" , ".sa", ".bwt", ".pac", ".ann" as secondary files if they are not present in the same location as the ".fasta" file
biometrics_plot	Whether to output biometrics plots.	true
biometrics_json	Whether to output biometrics results in JSON.	true
collapsed_biometrics_coverage_threshold	Coverage threshold for biometrics collapsed BAM calculations.	200
collapsed_biometrics_major_threshold	Major contamination threshold for biometrics collapsed BAM calculations.	1
collapsed_biometrics_min_base_quality	Minimum base quality threshold for biometrics collapsed BAM calculations.	1
collapsed_biometrics_min_coverage	Minimum coverage for a site to be included in biometrics collapsed BAM calculations.	10
collapsed_biometrics_min_homozygous_thresh	Minimum threshold to consider a site as homozygous in biometrics collapsed BAM calculations.	0.1
collapsed_biometrics_min_mapping_quality	Minimum mapping quality for biometrics collapsed BAM calculations.	10
collapsed_biometrics_minor_threshold	Minor contamination threshold used for biometrics collapsed BAM calculations.	0.02
duplex_biometrics_major_threshold	Major contamination threshold for biometrics duplex BAM calculations.	0.6
duplex_biometrics_min_base_quality	Minimum base quality threshold for biometrics duplex BAM calculations.	1
duplex_biometrics_min_coverage	Minimum coverage for a site to be included in biometrics duplex BAM calculations.	10
duplex_biometrics_min_homozygous_thresh	Minimum threshold to consider a site as homozygous in biometrics duplex BAM calculations.	0.1
duplex_biometrics_min_mapping_quality	Minimum mapping quality for biometrics duplex BAM calculations.	1
duplex_biometrics_minor_threshold	Minor contamination threshold used for biometrics duplex BAM calculations.	0.02
hsmetrics_coverage_cap	Read coverage max for CollectHsMetrics calculations.	30000
hsmetrics_minimum_base_quality	Minimum base quality for CollectHsMetrics calculations.	10
hsmetrics_minimum_mapping_quality	Minimum mapping quality for CollectHsMetrics calculations.	10
sequence_qc_min_basq	Minimum base quality threshold for sequence_qc calculations.	1
sequence_qc_min_mapq	Minimum mapping quality threshold for sequence_qc calculations.	1
sequence_qc_threshold	Noise threshold used for sequence_qc calculations.	0.002
sequence_qc_truncate	Whether to set the truncate parameter to True when using pysam.

Template Inputs File

inputs.yaml

biometrics_bed_file:
  class: File
  path: /path/to/MSK-ACCESS-v1_0-probe-B.sorted.bed
biometrics_json: true
biometrics_plot: true
biometrics_vcf_file:
  class: File
  path: /path/to/MSK-ACCESS-v1_0-TilingaAndFpSNPs.vcf
collapsed_bam:
- class: File
  path: /path/to/bam
collapsed_biometrics_coverage_threshold: null
collapsed_biometrics_major_threshold: null
collapsed_biometrics_min_base_quality: null
collapsed_biometrics_min_coverage: null
collapsed_biometrics_min_homozygous_thresh: null
collapsed_biometrics_min_mapping_quality: null
collapsed_biometrics_minor_threshold: null
duplex_bam:
- class: File
  path: /path/to/bam
duplex_biometrics_major_threshold: null
duplex_biometrics_min_base_quality: null
duplex_biometrics_min_coverage: null
duplex_biometrics_min_homozygous_thresh: null
duplex_biometrics_min_mapping_quality: null
duplex_biometrics_minor_threshold: null
group_reads_by_umi_bam:
- class: File
  path: /path/to/bam
hsmetrics_coverage_cap: 30000
hsmetrics_minimum_base_quality: 1
hsmetrics_minimum_mapping_quality: 1
noise_sites_bed:
  class: File
  path: /path/to/MSK-ACCESS-v1_0-probe-A_no_msi_sorted_deduped.bed
pool_a_bait_intervals:
  class: File
  path: /path/to/MSK-ACCESS-v1_0-probe-A_baits.sorted.interval_list
pool_a_target_intervals:
  class: File
  path: /path/to/MSK-ACCESS-v1_0_panelA_targets.interval_list
pool_b_bait_intervals:
  class: File
  path: /path/to/MSK-ACCESS-v1_0-probe-B_baits.sorted.interval_list
pool_b_target_intervals:
  class: File
  path: /path
reference:
  class: File
  path: /path
sample_group:
- patient_id
sample_name:
- sample_id
sample_sex:
- M
sample_type:
- tumor
sequence_qc_min_basq: 1
sequence_qc_min_mapq: 1
sequence_qc_threshold: null
sequence_qc_truncate: null
simplex_bam:
- class: File
  path: /path
uncollapsed_bam:
- class: File
  path: /path
uncollapsed_bam_base_recal:
- class: File
  path: /path