{
  "_id": "6aca8d38fe5cc25786e8b547",
  "Package": "RcwlPipelines",
  "Title": "Bioinformatics pipelines based on Rcwl",
  "Version": "1.28.0",
  "Authors@R": "c(person(given = \"Qiang\", family = \"Hu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"qiang.hu@roswellpark.org\"),\nperson(given = \"Qian\", family = \"Liu\",\nrole = c(\"aut\"),\nemail = \"qian.liu@roswellpark.org\"),\nperson(given = \"Shuang\", family = \"Gao\",\nrole = c(\"aut\"),\nemail = \"shuang.gao@roswellpark.org\"))",
  "Description": "A collection of Bioinformatics tools and pipelines based\non R and the Common Workflow Language.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "biocViews": "Software, WorkflowStep, Alignment, Preprocessing,\nQualityControl, DNASeq, RNASeq, DataImport, ImmunoOncology",
  "SystemRequirements": "nodejs",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "cmake libglpk-dev make libgit2-dev libicu-dev\nlibpng-dev libssh2-1-dev libuv1-dev libxml2-dev libssl-dev\npython3 libx11-dev zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:49:45 UTC",
  "RemoteUrl": "https://github.com/bioc/RcwlPipelines",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "01bab3cc8446560dca64bc08e4fc90a7af399909",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 18:00:07 UTC",
    "User": "root"
  },
  "Author": "Qiang Hu [aut, cre],\nQian Liu [aut],\nShuang Gao [aut]",
  "Maintainer": "Qiang Hu <qiang.hu@roswellpark.org>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "RcwlPipelines_1.28.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/654de2956b81117d02f6371039274477ac85f5ae77838d3c7634a5cfd8ced5e0",
  "_filesize": 117724,
  "_sha256": "654de2956b81117d02f6371039274477ac85f5ae77838d3c7634a5cfd8ced5e0",
  "_expires": "2027-01-18T19:08:37.000Z",
  "_created": "2026-10-10T18:00:07.000Z",
  "_published": "2026-10-10T19:08:40.008Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 11
  },
  "_upstream": "https://github.com/bioc/RcwlPipelines",
  "_commit": {
    "id": "01bab3cc8446560dca64bc08e4fc90a7af399909",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380585
  },
  "_maintainer": {
    "name": "Qiang Hu",
    "email": "qiang.hu@roswellpark.org",
    "login": "hubentu",
    "description": "",
    "uuid": 9856666
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114277172216,
      "time": 168,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11678426529"
    },
    {
      "job": 114277172085,
      "time": 317,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11677967665"
    },
    {
      "job": 114277172161,
      "time": 230,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11678311926"
    },
    {
      "job": 114277172165,
      "time": 151,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11679029733"
    },
    {
      "job": 114277172056,
      "time": 191,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11678874949"
    },
    {
      "job": 114276394204,
      "time": 235,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11677432887"
    },
    {
      "job": 114277172112,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11677592804"
    },
    {
      "job": 114277172138,
      "time": 180,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11678171983"
    },
    {
      "job": 114277172213,
      "time": 142,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11678376677"
    },
    {
      "job": 114277172157,
      "time": 165,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11678261853"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "Rcwl",
      "role": "Depends"
    },
    {
      "package": "BiocFileCache",
      "role": "Depends"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "git2r",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "workflowstep",
    "alignment",
    "preprocessing",
    "qualitycontrol",
    "dnaseq",
    "rnaseq",
    "dataimport",
    "immunooncology"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 401,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RcwlPipelines"
  },
  "_searchresults": 31,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RcwlPipelines.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Command",
    "Container",
    "cwlHub",
    "cwlInstall",
    "cwlLoad",
    "cwlSearch",
    "cwlUpdate",
    "mcols",
    "searchContainer",
    "show",
    "title",
    "Type"
  ],
  "_help": [
    {
      "page": "cwlHub-class",
      "title": "cwlHub",
      "topics": [
        "Command",
        "Container",
        "cwlHub",
        "cwlHub-class",
        "mcols,cwlHub-method",
        "show,cwlHub-method",
        "title",
        "Type",
        "[,cwlHub,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "cwlInstall",
      "title": "cwlInstall",
      "topics": [
        "cwlInstall"
      ]
    },
    {
      "page": "cwlLoad",
      "title": "cwlLoad",
      "topics": [
        "cwlLoad"
      ]
    },
    {
      "page": "cwlSearch",
      "title": "cwlSearch",
      "topics": [
        "cwlSearch"
      ]
    },
    {
      "page": "cwlUpdate",
      "title": "cwlUpdate",
      "topics": [
        "cwlUpdate"
      ]
    },
    {
      "page": "RcwlPipelines",
      "title": "RcwlPipelines",
      "topics": [
        "RcwlPipelines"
      ]
    },
    {
      "page": "searchContainer",
      "title": "seawrch containers",
      "topics": [
        "searchContainer"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RcwlPipelines/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "askpass",
    "backports",
    "base64enc",
    "base64url",
    "basilisk",
    "batchtools",
    "BH",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "brew",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "clipr",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DiagrammeR",
    "digest",
    "dir.expiry",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "git2r",
    "glue",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppTOML",
    "Rcwl",
    "readr",
    "reticulate",
    "rlang",
    "rmarkdown",
    "rprojroot",
    "RSQLite",
    "rstudioapi",
    "S4Vectors",
    "sass",
    "scales",
    "shiny",
    "snow",
    "sourcetools",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "visNetwork",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "RcwlPipelines.Rmd",
      "filename": "RcwlPipelines.html",
      "title": "RcwlPipelines: Bioinformatics tools and pipelines based on Rcwl",
      "author": "Qiang Hu, Qian Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Project resources",
        "The R recipes and cwl scripts",
        "Tutorial book",
        "RcwlPipelines core functions",
        "cwlUpdate",
        "cwlSearch",
        "cwlLoad",
        "Customize a tool or pipeline",
        "Run a tool or pipeline",
        "SessionInfo"
      ],
      "created": "2019-03-01 16:03:11",
      "modified": "2021-02-25 04:03:06",
      "commits": 17
    }
  ],
  "_score": 5.144574207609616,
  "_indexed": false,
  "_nocasepkg": "rcwlpipelines",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/RcwlPipelines",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-10-10T18:04:28.000Z",
      "distro": "resolute",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/b16244ce92f1e6cc6cb5f25f47a6d5c5a1c2cf0bf54230e6bea60f2b07dbff51",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-10-10T18:03:29.000Z",
      "distro": "resolute",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/d612263f7f92febced20b54446c0405f31402048ed5b6abb9669249a73bad90a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-10-10T19:06:59.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/ef65df7f40a09138eec35feb80a99bf8aad78898a15ebc0e07d58d8310c823d4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-10-10T19:07:03.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/76ce02ab136c5278e2fc54dbc0dd43fd987ce248a429f6cb066a32442d862a7c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.28.0",
      "date": "2026-10-10T18:02:30.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/d9c57e4e73008e6e591bb8a7c2a60913b022e56bd610f61cd7421d6507e09205",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-10T18:02:06.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/9f23e7e220da2929395b01ebb84c3bbe3100a9afa6084024121d31d8d6095f89",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-10T18:01:42.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/078426f6509cc922e32e2828a7692be96584aa9677c651ec7419a2862f108850",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-10-10T18:01:44.000Z",
      "commit": "01bab3cc8446560dca64bc08e4fc90a7af399909",
      "fileid": "https://r2.ropensci.org/90082003f4d8ef775dfe950c06f4df775ee3c29827e33bc8286920a004280b88",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38073759227"
    }
  ]
}