Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/nci-gdc/aliquot-maf-cwl

CWL tools and workflows for generating and processing aliquot-MAF
https://github.com/nci-gdc/aliquot-maf-cwl

bioinformatics cwl maf-files workflow

Last synced: 6 days ago
JSON representation

CWL tools and workflows for generating and processing aliquot-MAF

Host: GitHub
URL: https://github.com/nci-gdc/aliquot-maf-cwl
Owner: NCI-GDC
License: apache-2.0
Created: 2019-01-17T18:57:51.000Z (almost 6 years ago)
Default Branch: main
Last Pushed: 2024-03-06T17:46:22.000Z (10 months ago)
Last Synced: 2024-04-14T12:44:36.363Z (9 months ago)
Topics: bioinformatics, cwl, maf-files, workflow
Language: Common Workflow Language
Size: 62.5 KB
Stars: 0
Watchers: 10
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # aliquot-maf-cwl

CWL tools and workflows for generating and processing aliquot-MAF

## Convert annotated VCF to an aliquot MAF

Workflow: `workflows/vcf_to_aliquot_maf_wf.cwl`

**Inputs**

| Input | Type | Description |

| ----- | ---- | ----------- |

| annotated_vcf_uuid | uuid | input vcf uuid |

| annotated_vcf_index_uuid | uuid | input vcf index uuid |

| bioclient_config | file | bioclient config file |

| biotype_priority_uuid | uuid | biotype priority json uuid |

| caller_id | string | variant caller id |

| case_uuid | uuid | case uuid |

| context_size | int | reference context size (_5_) |

| cosmic_vcf_uuid | uuid | cosmic vcf uuid |

| cosmic_vcf_index_uuid | uuid | cosmic vcf index uuid|

| custom_enst_uuid | uuid | custom transcript overloads file uuid |

| dbsnp_priority_db_uuid | uuid | dbSNP priority sqlite uuid |

| effect_priority_uuid | uuid | effect prioty json uuid |

| exac_freq_cutoff | float | non-tcga exac frequency filter cutoff (_0.001_) |

| experimental_strategy | string | experimental strategy |

| gdc_blacklist_uuid | uuid | blacklist uuid if doing blacklist filter |

| gdc_pon_vcf_uuid | uuid | panel of normals vcf uuid |

| gdc_pon_vcf_index_uuid | uuid | panel of normals vcf index uuid |

| hotspot_tsv_uuid | uuid | hotspot tsv uuid |

| job_uuid | uuid | uuid of the workflow job |

| maf_center | string[] | list of sequencing centers |

| min_n_depth | int | normal depth filtering cutoff (_7_) |

| non_tcga_exac_vcf_uuid | uuid | Non-TCGA ExAC vcf uuid |

| non_tcga_exac_vcf_index_uuid | uuid | Non-TCGA ExAC vcf index uuid |

| nonexonic_intervals_uuid | uuid | Exonic regions bed uuid|

| nonexonic_intervals_index_uuid | uuid | Exonic regions bed tabix index uuid |

| normal_aliquot_uuid | uuid | normal aliquot uuid |

| normal_bam_uuid | uuid | normal sample's bam uuid |

| normal_submitter_id | string | normal aliquot's submitted id |

| reference_fasta_index_uuid | uuid | main chromosome reference fai uuid |

| reference_fasta_uuid | uuid | main chromosome reference fasta uuid |

| sequencer | string[] | list of sequencers used |

| target_intervals_record | indexed_file[]| list of targeted sequencing `indexed_file` objects |

| tumor_aliquot_uuid | uuid | tumor aliquot uuid |

| tumor_bam_uuid | uuid | tumor aliquot's bam uuid |

| tumor_submitter_id | string | tumor aliquot's submitter id |

| upload_bucket | string | upload bucket uri |

An `indexed_file` object id defined as:

```

{

  "main_file_uuid": "",

  "index_file_uuid": ""

}

```

**Outputs**

* `aliquot_maf_uuid` - the UUID of the generated aliquot MAF file

## Aggregate/merge aliquot MAF from different callers

Workflow: `workflows/ensemble_aliquot_maf_wf.cwl`

**Inputs**

| Input | Type | Description |

| ----- | ---- | ----------- |

| aliquot_maf_uuid_list | optional_file_uuid[] | input list of `optional_file_uuid` objects |

| bioclient_config | file | bioclient config file |

| experimental_strategy | string | experimental strategy |

| job_uuid | uuid | uuid of the workflow job |

| min_callers | int | minimum number of callers supporting the variant for masked merged maf file (_2_) |

| min_n_depth | float | minimal Normal depth cutoff after averaging (_7_) |

| upload_bucket | string | upload bucket uri |

An `optional_file_uuid` object:

```

{

    "key": "",

    "uuid": ""

}

```

**Outputs**

* `aliquot_merged_raw_maf_uuid` - the UUID of the raw merged MAF

* `aliquot_merged_masked_maf_uuid` - the UUID of the masked merged MAF

* `aliquot_maf_metrics_uuid` - the UUID of the metrics JSON file