services.json

{
    "assembly_annotation": {
        "label": "",
        "template": "assembly",
        "url": "",
        "order": 1,
        "begin": "",
        "end": "",
        "description": "Nextflow assembly pipeline to assemble bacterial genomes",
        "clean": {
          "folders":["03-assembly/trimming/trimmed", "01-preprocessing", "work"],
          "files":[""]
        },
        "no_copy": ["RAW", "TMP"]
    },
    "mtbseq": {
        "label": "",
        "template": "mtbseq",
        "order": 1,
        "begin": "base",
        "end": "mag_met",
        "url": "https://github.com/ngs-fzb/MTBseq_source",
        "description": "Mycobacterium tuberculosis mapping, variant calling and detection of resistance using MTBseq",
        "clean": {
          "folders":["03-assembly/trimming/trimmed", "01-preprocessing", "work"],
          "files":[""]
        },
        "no_copy": ["RAW", "TMP"]
    },
    "wgmlst_taranis": {
        "label": "",
        "template": "taranis",
        "order": 1,
        "begin": "base",
        "end": "mag_met",
        "url": "https://github.com/BU-ISCIII/taranis",
        "description": "Multilocus sequence typing (MLST) using Taranis",
        "depends_on": "assembly_annotation",
        "clean": {
          "folders":["03-assembly/trimming/trimmed", "01-preprocessing", "work"],
          "files":[""]
        },
        "no_copy": ["RAW", "TMP"]
    },
    "wgmlst_chewbbaca": {
        "label": "",
        "template": "chewbbaca",
        "order": 1,
        "begin": "base",
        "end": "mag_met",
        "url": "https://github.com/B-UMMI/chewBBACA",
        "description": "Multilocus sequence typing (MLST) using chewBBACA",
        "depends_on": "assembly_annotation",
        "clean": {
          "folders":["03-assembly/trimming/trimmed", "01-preprocessing/{sample_name}", "work"],
          "files":[""]
        },
        "no_copy": ["RAW", "TMP"]
    },
    "sars_viralrecon": {
        "label": "",
        "template": "sars_viralrecon",
        "url": "https://github.com/BU-ISCIII/viralrecon",
        "order": 1,
        "begin": "",
        "end": "mag_met",
        "description": "Viral genome reconstruction analysis for SARS-COV-2 data",
        "clean": {
          "folders":["work"],
          "files":["variants/bowtie2/sample_name.sorted.bam","variants/bowtie2/sample_name.sorted.bam.bai"]
        },
        "no_copy": ["RAW", "TMP"]
    }
}