---
description: Input files and parameters required to run workflow
---

# Inputs Description

{% hint style="warning" %}
Common workflow language execution engines accept two types of input that are [JSON](https://json.org) or [YAML](https://yaml.org), 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/](http://www.commonwl.org/user_guide/yaml/)
{% endhint %}

## 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

{% code title="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
```
{% endcode %}
