dxapp.json

{
  "name": "eggd_vcf_handler_for_uranus",
  "title": "eggd_vcf_handler_for_uranus",
  "summary": "Annotates and filters VCF files for Uranus",
  "dxapi": "1.0.0",
  "openSource": true,
  "version": "2.8.0",
  "inputSpec": [
    {
      "name": "mutect2_vcf",
      "label": "gzipped mutect2 vcf",
      "help": "mutect2 vcf",
      "class": "file",
      "patterns": ["*.vcf.gz"],
      "optional": false
    },
    {
      "name": "pindel_vcf",
      "label": "gzipped pindel vcf",
      "help": "pindel vcf",
      "class": "file",
      "patterns": ["*.vcf.gz"],
      "optional": false
    },
    {
      "name": "pindel_vcf_idx",
      "label": "index of pindel vcf",
      "help": "pindel vcf index",
      "class": "file",
      "patterns": ["*.vcf.gz.tbi"],
      "optional": false
    },
    {
      "name": "mutect2_bed",
      "label": "bed file used to define regions of interest of mutect2 output vcf",
      "help": "The bed file will be used to remove variants outside the regions of interest",
      "class": "file",
      "patterns": ["coding_unrestricted*.bed"],
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/bed_files/b38/kits/myeloid"
        }
      ],
      "optional": false
    },
    {
      "name": "pindel_bed",
      "label": "pindel regions bed file",
      "help": "The bed file will be used to remove variants outside the regions of interest",
      "class": "file",
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/bed_files/b38/kits/myeloid"
        }
      ],
      "optional": false
    },
    {
      "name": "mutect2_fasta",
      "label": "FASTA for bcftools to split multiallelics",
      "help": "Should be equivalent FASTA as used by mutect2",
      "class": "file",
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/genomes/b38"
        }
      ],
      "optional": false
    },
    {
      "name": "mutect2_fai",
      "label": "mutect2 fai index",
      "help": "Should be equivalent fai index as used by mutect2",
      "class": "file",
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/genomes/b38"
        }
      ],
      "optional": false
    },
    {
      "name": "vep_docker",
      "label": "VEP docker image",
      "help": "compressed docker image of VEP",
      "class": "file",
      "patterns": ["*docker.tar.gz"],
      "optional": false,
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/assets/vep/vep_docker_v103.1/"
        }
      ]
    },
    {
      "name": "vep_plugins",
      "label": "plugin files for VEP",
      "help": "Associated plugin files for VEP",
      "class": "array:file",
      "optional": false,
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/assets/vep/vep_docker_v103.1/"
        }
      ]
    },
    {
      "name": "vep_refs",
      "label": "reference sources for VEP",
      "help": "Reference file annotation sources for VEP (not ClinVar etc.)",
      "class": "array:file",
      "optional": false,
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/annotation/b38/vep/"
        }
      ]
    },
    {
      "name": "vep_annotation",
      "label": "annotation sources for VEP",
      "help": "Reference file annotation sources for VEP and index (ClinVar & CADD)",
      "class": "array:file",
      "optional": false,
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/annotation/b38/"
        }
      ]
    },
    {
      "name": "maf_file",
      "label": "MAF file",
      "help": "MAF file created from Myeloid samples sequenced on NovaSeqs",
      "class": "file",
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/annotation/b38/haemonc/novaseq_allele_frequencies"
        }
      ]
    },
    {
      "name": "maf_file_tbi",
      "label": "MAF file index",
      "help": "index of MAF file",
      "class": "file",
      "suggestions": [
        {
          "name": "001_Reference",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/annotation/b38/haemonc/novaseq_allele_frequencies"
        }
      ]
    }
  ],
  "outputSpec": [
    {
      "name": "pindel_vep_vcf",
      "label": "Annotated cgppindel VCF",
      "help": "VCF that has been previously filtered and now annotated with VEP",
      "class": "file"
    },
    {
      "name": "allgenes_filtered_vcf",
      "label": "Filtered and annotated VCF for all panel genes",
      "help": "VCF that has been filtered and annotated using bedtools, bcftools and VEP",
      "class": "file",
      "patterns": ["*allgenesvep.vcf"]
    },
    {
      "name": "bsvi_vcf",
      "label": "modified vcf for bsvi",
      "help": "invalid vcf for bsvi workaround",
      "class": "file",
      "patterns": ["*_allgenes_bsvi.vcf"]
    },
    {
      "name": "text_report",
      "label": "Text variant report from all genes",
      "help": "Text (tsv) list of variants from all genes",
      "class": "file",
      "patterns": ["*_allgenes.tsv"]
    },
    {
      "name": "excel_report",
      "label": "Excel variant report for scientists",
      "help": "Excel workbook with variants for each panel in separate sheets",
      "class": "file",
      "patterns": ["*_panels.xlsx"]
    }
  ],
  "runSpec": {
    "interpreter": "bash",
    "timeoutPolicy": {
      "*": {
        "hours": 6
      }
    },
    "distribution": "Ubuntu",
    "release": "20.04",
    "version": "0",
    "file": "src/code.sh",
    "assetDepends": [
      {
        "name": "bedtools",
        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
        "folder": "/app_assets/bedtools/bedtools_v2.30.0",
        "version": "2.30.0"
      },
      {
        "name": "htslib",
        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
        "folder": "/app_assets/htslib/htslib_v1.12.0",
        "version": "1.12.0"
      },
      {
        "name": "python_packages",
        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
        "folder": "/app_assets/python_packages/python_packages_v1.1.0",
        "version": "1.1.0"
      }
    ]
  },
  "authorizedUsers": [
    "org-emee_1"
  ],
  "regionalOptions": {
    "aws:eu-central-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem1_ssd2_v2_x4"
        }
      }
    }
  },
  "details": {
    "citations": [
      "doi:10.1093/bioinformatics/btp352",
      "doi:10.1093/bioinformatics/btq033",
      "doi:10.1186/s13059-016-0974-4",
      "doi:10.1186/s13073-021-00835-9"
    ],
    "upstreamProjects": [
      {
        "name": "bcftools",
        "repoUrl": "https://github.com/samtools/bcftools",
        "version": "1.11",
        "license": "MIT/Expat",
        "licenseUrl": "https://github.com/samtools/bcftools/blob/1.11/LICENSE",
        "author": "samtools"
      },
      {
        "name": "bedtools",
        "repoUrl": "https://github.com/arq5x/bedtools2",
        "version": "2.29.2",
        "license": "MIT",
        "licenseUrl": "https://github.com/arq5x/bedtools2/blob/v2.29.2/LICENSE",
        "author": "Quinlan Laboratory at the University of Virginia"
      },
      {
        "name": "bgzip",
        "repoUrl": "https://github.com/samtools/htslib",
        "version": "1.11",
        "license": "MIT/Expat",
        "licenseUrl": "https://github.com/samtools/htslib/blob/1.11/LICENSE",
        "author": "samtools"
      },
      {
        "name": "samtools",
        "repoUrl": "https://github.com/samtools/samtools",
        "version": "1.11",
        "license": "MIT/Expat",
        "licenseUrl": "https://github.com/samtools/samtools/blob/1.11/LICENSE",
        "author": "samtools"
      },
      {
        "name": "tabix",
        "repoUrl": "https://github.com/samtools/htslib",
        "version": "1.11",
        "license": "MIT/Expat",
        "licenseUrl": "https://github.com/samtools/htslib/blob/1.11/LICENSE",
        "author": "samtools"
      },
      {
        "name": "VEP",
        "repoUrl": "https://github.com/Ensembl/ensembl-vep",
        "version": "130.1",
        "license": "Apache License 2.0",
        "licenseUrl": "https://github.com/Ensembl/ensembl-vep/blob/release/103/LICENSE",
        "author": "EMBL-EBI"
      }
    ],
    "contactEmail": "East GLH Bioinformatics",
    "whatsNew": "*2.8.0 Remove default input resource files \n * 2.6.1 Change SampleName field in openCGA VCF header to be first field of filename\n *2.6.0 Add 15 new genes, 2 new panels and able to handle multiple transcripts for a given gene \n * 2.5.2 Bug fix for wrongly raised AssertionError \n * 2.5.1 Fix bug on not removing .gz suffix from opencga vcfs; * 2.5.0 Add extra output VCFs with modified headers to include sample ID for uploading to openCGA \n * 2.4.0 Add filtering to myeloid tab of synonymous and common variants; Remove depcrecated transcript for CHEK2 \n * 2.3.0 Add custom annotation for Cosmic (fixes bug with multiple IDs added); Add filtering and annotation for pindel; Split annotation sources to separate inputs \n * 2.2.0 New MAF file as input; Refactoring \n * 2.1.0 Sample names added\n * 2.0.0 New panels; VEP input; previous counts\n * 1.5.7 Add CADD and ClinVar annotation\n * 1.5.3 Added excel workbook output with variants for each panel in separate sheets, removed synonymous variant filter, prefix exon numbers with the word exon to overcome excel, further report_text formatting\n * 1.4.12 Allele fraction in tsv variantlist\n * 1.4.10 Make mark-section and mark-success executable in github\n * 1.4.9 Minor changed to report_text field in tsv, and brings back gnomad AF in tsv(!)\n * 1.4.8 (Deprecated) Adds AF column to text report\n * 1.4.4 (Deprecated) Uses app assets\n * 1.3.4 (Deprecated) Creates text report\n * 1.2.10 (Deprecated) Creates BSVI VCF\n * 1.1.9 (Deprecated) With VEP\n * 1.0.0 (Deprecated) Initial app"
  },
  "categories": [],
  "developers":[
    "org-emee_1"
  ],
  "access": {
    "network": [
      "*"
    ],
    "project": "UPLOAD"
  },
  "ignoreReuse": true
}