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

Template Inputs File

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.

collapsed_biometrics_min_base_quality

Minimum base quality threshold for biometrics collapsed BAM calculations.

collapsed_biometrics_min_coverage

Minimum coverage for a site to be included in biometrics collapsed BAM calculations.

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.

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.

duplex_biometrics_min_coverage

Minimum coverage for a site to be included in biometrics duplex BAM calculations.

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.

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.

hsmetrics_minimum_mapping_quality

Minimum mapping quality for CollectHsMetrics calculations.

sequence_qc_min_basq

Minimum base quality threshold for sequence_qc calculations.

sequence_qc_min_mapq

Minimum mapping quality threshold for sequence_qc calculations.

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.

Base-recalibrated uncollapsed BAM file.(Required)

Collapsed BAM file.(Required)

group_reads_by_umi_bam

Collapsed BAM file produced by fgbio's GroupReadsByUmi tool.(Required)

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

Duplex BAM file.(Required)

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

Inputs Description

hashtagParameter Used by Tools

hashtagCommon Parameters Across Tools

hashtagTemplate Inputs File

Inputs Description

hashtagParameter Used by Tools

hashtagCommon Parameters Across Tools

hashtagTemplate Inputs File

Parameter Used by Tools

Common Parameters Across Tools

Template Inputs File

Parameter Used by Tools

Common Parameters Across Tools

Template Inputs File