[
    {
        "id": "vcf_plot_dv",
        "name": "Plot VCF (deepvariant)",
        "description": "Plot VCF stats with deepvariant",
        "version": "0.9.0",
        "website": "https:\/\/github.com\/google\/deepvariant",
        "git": "https:\/\/github.com\/google\/deepvariant",
        "documentation": "https:\/\/github.com\/google\/deepvariant\/blob\/r0.9\/docs\/README.md",
        "article": "10.1038\/nbt.4235",
        "multiqc": "plot_vcf_dv_iframes",
        "commands": [
            {
                "name": "vcf_plot_dv",
                "cname": "Plot VCF (deepvariant)",
                "command": null,
                "category": "vcf_postprocess",
                "output_dir": "vcf_plot_dv",
                "inputs": [
                    {
                        "name": "vcfs",
                        "type": "vcf"
                    }
                ],
                "outputs": [
                    {
                        "name": "List of plots files",
                        "type": "tsv",
                        "file": "vcf_plots_mqc_list.tsv",
                        "description": "List of plots files generated and included in the final report"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "deepvariant": [
                "A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology 36, 983-987 (2018). Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T. Afshar, Sam S. Gross, Lizzie Dorfman, Cory Y. McLean, Mark A. DePristo, doi: https:\/\/doi.org\/10.1038\/nbt.4235"
            ]
        },
        "yaml": "{\n  id: vcf_plot_dv,\n  name: Plot VCF (deepvariant),\n  description: \"Plot VCF stats with deepvariant\",\n  version: \"0.9.0\",\n  website: \"https:\/\/github.com\/google\/deepvariant\",\n  git: \"https:\/\/github.com\/google\/deepvariant\",\n  documentation: \"https:\/\/github.com\/google\/deepvariant\/blob\/r0.9\/docs\/README.md\",\n  article: 10.1038\/nbt.4235,\n  multiqc: \"plot_vcf_dv_iframes\",\n  commands:\n    [\n      {\n        name: vcf_plot_dv,\n        cname: \"Plot VCF (deepvariant)\",\n        command: ~,\n        category: \"vcf_postprocess\",\n        output_dir: vcf_plot_dv,\n        inputs: [{ name: vcfs, type: \"vcf\" }],\n        outputs: [\n          { name: \"List of plots files\", type: \"tsv\", file: \"vcf_plots_mqc_list.tsv\", description: \"List of plots files generated and included in the final report\" }\n        ],\n        options:\n          [\n          ],\n      },\n    ],\n  install: {\n    # deep_variant_part1: [\n    #   #clone deepvariant git\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/google\/deepvariant\/archive\/v0.9.0.tar.gz\",\n    #   \"tar -xvzf v0.9.0.tar.gz\",\n    #   \"mv deepvariant-0.9.0 \/opt\/deepvariant\",\n    #   \"sed -i \\\"\/sudo -H apt-get -qq -y install python-dev python-pip python-wheel > \\\\\/dev\\\\\/null\/d\\\" \/opt\/deepvariant\/run-prereq.sh\",\n    #   \"sed -i \\\"\/python -m pip install .* --upgrade --force-reinstall pip\/d\\\"\\ \/opt\/deepvariant\/run-prereq.sh\",\n    # ],\n    # deep_variant_part2: [\n    #   # install virtualenv\n    #   \"cd \/opt\/deepvariant\",\n    #   \"apt-get install -y python-dev python-pip\",\n    #   \"pip install virtualenv\",\n    #   \"virtualenv -p \/usr\/bin\/python2.7 deepvariant_env\",\n    #   \"\/bin\/bash -c \\\"source deepvariant_env\/bin\/activate && pip install pip==19.3.1\\\"\",\n    # ],\n    # deep_variant_part3: [\n    #   # install dependencies and build sources\n    #   \"cd \/opt\/deepvariant\",\n    #   \"\/bin\/bash -c \\\"source deepvariant_env\/bin\/activate && PYTHONPATH=\/opt\/deepvariant\/deepvariant_env\/lib\/python2.7 .\/build-prereq.sh\\\"\",\n    #   \"\/bin\/bash -c \\\"source deepvariant_env\/bin\/activate && PATH=\\\"${HOME}\/bin:${PATH}\\\" .\/build_release_binaries.sh\\\"\"\n    # ],\n    # deep_variant_part4: [\n    #   \"cd \/opt\",\n    #   \"cp \/opt\/deepvariant\/bazel-genfiles\/licenses.zip .\",\n    #   \"mkdir \/opt\/deepvariant\/bin\/\",\n    #   \"cd \/opt\/deepvariant\/bin\/\",\n    #   \"cp \/opt\/deepvariant\/run-prereq.sh .\",\n    #   \"cp \/opt\/deepvariant\/settings.sh .\",\n    #   \"cp \/opt\/deepvariant\/bazel-bin\/deepvariant\/make_examples.zip .\",\n    #   \"cp \/opt\/deepvariant\/bazel-bin\/deepvariant\/call_variants.zip .\",\n    #   \"cp \/opt\/deepvariant\/bazel-bin\/deepvariant\/postprocess_variants.zip .\",\n    #   \"cp \/opt\/deepvariant\/bazel-bin\/deepvariant\/model_train.zip .\",\n    #   \"cp \/opt\/deepvariant\/bazel-bin\/deepvariant\/model_eval.zip .\",\n    #   \"cp \/opt\/deepvariant\/scripts\/run_deepvariant.py .\",\n    #   \"\/bin\/bash -c \\\"source \/opt\/deepvariant\/deepvariant_env\/bin\/activate && .\/run-prereq.sh\\\"\",\n    # ],\n    # deep_variant_part5: [\n    #   \"BASH_HEADER='#!\/bin\/bash'\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python \/opt\/deepvariant\/bin\/make_examples.zip \\\"$@\\\"' > \/opt\/deepvariant\/bin\/make_examples\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python \/opt\/deepvariant\/bin\/call_variants.zip \\\"$@\\\"' > \/opt\/deepvariant\/bin\/call_variants\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python \/opt\/deepvariant\/bin\/postprocess_variants.zip \\\"$@\\\"' > \/opt\/deepvariant\/bin\/postprocess_variants\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python \/opt\/deepvariant\/bin\/model_train.zip \\\"$@\\\"' > \/opt\/deepvariant\/bin\/model_train\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python \/opt\/deepvariant\/bin\/model_eval.zip \\\"$@\\\"' > \/opt\/deepvariant\/bin\/model_eval\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python -u \/opt\/deepvariant\/bin\/run_deepvariant.py \\\"$@\\\"' > \/opt\/deepvariant\/bin\/run_deepvariant\",\n    #   \"printf \\\"%s\\\\n%s\\\\n\\\" \\\"${BASH_HEADER}\\\" 'python -u \/opt\/deepvariant\/bin\/vcf_stats_report.py \\\"$@\\\"' > \/opt\/deepvariant\/bin\/vcf_stats_report\",\n    #   \"chmod +x \/opt\/deepvariant\/bin\/make_examples \/opt\/deepvariant\/bin\/call_variants \/opt\/deepvariant\/bin\/postprocess_variants \/opt\/deepvariant\/bin\/model_train \/opt\/deepvariant\/bin\/model_eval \/opt\/deepvariant\/bin\/run_deepvariant\",\n\n    #   \"mkdir \/opt\/bin\",\n    #   \"cd \/opt\/bin\",\n    #   \"wget https:\/\/github.com\/dnanexus-rnd\/GLnexus\/releases\/download\/v1.2.1\/glnexus_cli\",\n    #   \"wget https:\/\/raw.githubusercontent.com\/dnanexus-rnd\/GLnexus\/v1.2.1\/LICENSE -O glnexus_cli.LICENSE\",\n    #   \"chmod +rx \/opt\/bin\/glnexus_cli\",\n\n    #   \"mkdir \/opt\/models\",\n    #   \"mkdir \/opt\/models\/wgs\",\n    #   \"cd \/opt\/models\/wgs\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wgs_standard\/model.ckpt.data-00000-of-00001\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wgs_standard\/model.ckpt.index\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wgs_standard\/model.ckpt.meta\",\n    #   \"chmod +r \/opt\/models\/wgs\/model.ckpt*\",\n\n    #   \"mkdir \/opt\/models\/wes\",\n    #   \"cd \/opt\/models\/wes\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wes_standard\/model.ckpt.data-00000-of-00001\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wes_standard\/model.ckpt.index\",\n    #   \"wget https:\/\/storage.googleapis.com\/deepvariant\/models\/DeepVariant\/0.9.0\/DeepVariant-inception_v3-0.9.0+data-wes_standard\/model.ckpt.meta\",\n    #   \"chmod +r \/opt\/models\/wes\/model.ckpt*\",\n\n    #   \"apt-get -y update\",\n    #   \"apt-get install -y parallel\",\n    #   \"\/bin\/bash -c \\\"source \/opt\/deepvariant\/deepvariant_env\/bin\/activate && python -m pip install pip==9.0.3 && pip install absl-py==0.7.1\\\"\"\n    # ],\n    # mbb_mqc_plugin:\n    # [\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/mmassaviol\/mbb_mqc_plugin.git\",\n    #   \"cd mbb_mqc_plugin\",\n    #   \"python3 setup.py install\"\n    # ]\n  },\n  citations:  {\n    deepvariant: [\n      \"A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology 36, 983-987 (2018). Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T. Afshar, Sam S. Gross, Lizzie Dorfman, Cory Y. McLean, Mark A. DePristo, doi: https:\/\/doi.org\/10.1038\/nbt.4235\"\n    ],\n  }\n}\n"
    }
]