workflows.json

{
  "workflows":{
    "bactopia": {
      "description": "Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!",
      "repo": "bactopia/bactopia",
      "default_branch": "master",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    },
    "cecret": {
      "description": "Cecret is a workflow developed by @erinyoung at the Utah Public Health Laborotory for SARS-COV-2 sequencing with the artic/Illumina hybrid library prep workflow for MiSeq data.",
      "repo": "UPHL-BioNGS/Cecret",
      "default_branch": "master",
      "configuration": "configs/cecret_config_template.config",
      "schema":"nextflow_schema.json"
    },
    "donut_falls": {
      "description": "Donut Falls is a basic assembly workflow for Nanopore sequencing.",
      "repo": "UPHL-BioNGS/Donut_Falls",
      "default_branch": "main",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    },
    "dryad": {
      "description": "Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks. Dryad will performs both a reference free core-genome and/or a SNP analysis using the CFSAN-SNP pipeline.",
      "repo": "wslh-bio/dryad",
      "default_branch": "main",
      "configuration": "dryad.config",
      "schema":"nextflow_schema.json"
    },
    "grandeur": {
      "description": "Grandeur is short-read de novo assembly pipeline with serotyping.",
      "repo": "UPHL-BioNGS/Grandeur",
      "default_branch": "main",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    },
    "mycosnp": {
      "description": "MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris.",
      "repo": "CDCgov/mycosnp-nf",
      "default_branch": "master",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    },
    "phoenix": {
      "description": "PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens.",
      "repo": "CDCgov/phoenix",
      "default_branch": "main",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    },
    "spriggan": {
      "description": "Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.",
      "repo": "wslh-bio/spriggan",
      "default_branch": "main",
      "configuration": "spriggan.config",
      "schema":"nextflow_schema.json"
    },
    "viralrecon": {
      "description": "Viralrecon is a pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples.",
      "repo": "nf-core/viralrecon",
      "default_branch": "master",
      "configuration": "nextflow.config",
      "schema":"nextflow_schema.json"
    }
  }
}