https://github.com/nci-gdc/gdc-sanger-somatic-cwl

CWL Workflows for the Sanger Somatic Workflow
https://github.com/nci-gdc/gdc-sanger-somatic-cwl

bioinformatics cwl workflow

Last synced: 6 days ago
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CWL Workflows for the Sanger Somatic Workflow

• Host: GitHub
• URL: https://github.com/nci-gdc/gdc-sanger-somatic-cwl
• Owner: NCI-GDC
• License: apache-2.0
• Created: 2019-07-09T15:46:33.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2023-11-08T18:58:35.000Z (about 1 year ago)
• Last Synced: 2024-04-14T12:44:38.638Z (9 months ago)
• Topics: bioinformatics, cwl, workflow
• Language: Common Workflow Language
• Size: 75.2 KB
• Stars: 0
• Watchers: 10
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# GDC Sanger Somatic Variant Calling Workflow

This workflow takes a pair of harmnonized WGS BAM files and processes them through the

[CGP core WGS analysis](https://github.com/cancerit/dockstore-cgpwgs).

The docker images used in this workflow can be found in `current_docker_list.txt`.

## External Users

The entrypoint CWL workflow for external users in `workflows/subworkflows/main_gdc_wgs_workflow.cwl`.

The example of input json in `example/main_gdc_wgs_workflow.example.input.json`.

### Inputs

| Name | Type | Description |

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

| `sanger_threads` | `int?` | Max threads to use for parallel processes. |

| `other_threads` | `int?` | Number of threads to use for pindel, samtools, etc. |

| `job_uuid` | `string` | string use as a prefix for all the output filenames |

| `tumor_aliquot_uuid` | `string` | tumor sample uuid |

| `normal_aliquot_uuid` | `string` | normal sample uuid |

| `gdc_reference` | `File` | GDC reference fasta |

| `sequence_dict` | `File` | GDC reference sequence dictionary |

| `reference_fai` | `File` | GDC reference faidx index |

| `core_reference_tar` | `File` | Archive containing sanger reference files |

| `vagrent_cache` | `File` | Archive containing vagrent cache files |

| `snv_indel_tar` | `File` | Archive containing SNV/InDel data files for sanger workflow |

| `cnv_sv_tar` | `File` | Archive containing CNV/SV data files for sanger workflow |

| `qcset_tar` | `File` | Archive containing QC data files for sanger workflow |

| `tumor_bam` | `File` | Tumor bam file |

| `tumor_index` | `File` | Tumor bam index file |

| `normal_bam` | `File` | Normal bam file |

| `normal_index` | `File` | Normal bam index file |

The `core_reference_tar`, `vagrent_cache`, `snv_indel_tar`, `cnv_sv_tar`, and `qcset_tar` were sourced

from [here](https://github.com/cancerit/dockstore-cgpwgs/wiki/Reference-archives).

### Outputs

| Name | Type | Description |

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

| `wf_archive_file` | `File` | Archive of raw outputs |

| `brass_vcf_file` | `File` | Formatted brass VCF |

| `brass_vcf_index_file` | `File` | Formatted brass VCF index |

| `brass_bedpe_file` | `File` | Formatted brass bedpe |

| `brass_bedpe_index_file` | `File` | Formatted brass bedpe index |

| `caveman_vcf_file` | `File` | Formatted CaVEMan VCF |

| `caveman_vcf_index_file` | `File` | Formatted CaVEMand VCF index |

| `ascat_tumor_ploidy` | `float` | Estimated tumor ploidy |

| `ascat_tumor_purity` | `float` | Estimated tumor purity |

| `ascat_segmentation_file` | `File` | Formatted ASCAT CNV segmentation file |

| `ascat_genelevel_file` | `File` | Formatted ASCAT gene-level CNV file |

| `pindel_vcf` | `File` | Formatted Pindel VCF |

| `pindel_vcf_index` | `File` | Formatted Pindel VCF index |

## GDC Users

The entrypoint CWL workflow for GDC internal users is `workflows/gdc_sanger_wgs_somatic_workflow.cwl`.