Inventory (*.CFG) file format

The detailed description of inventory file format is a part of annotation pipeline project, so here is a short description covering details important for Anfisa project:

• Main principle of inventory files usage: these files are the same for almost all datasets, so there is a generic variant of such a file. But in reality some cases might differ to each other, so there is an option to slightly modify prototype of such a file in particular case.

• Most part of information in inventory file is part of annotation pipeline process. The only two information portion is used in Anfisa itself:

  • location of annotation json file<annotation json files> as main result of annotation process, as well as a main source file for dataset in Anfisa

  • supporting documentation for the case, in human readable formats: HTML and PNG, see the example (i.e. generic content) of inventory file, section "doc" for details.

• Format of inventory is a JSON format with some advanced features:

  • // comments are available

  • macro replacement schema is supported:

    • the macros ${DIR} and ${NAME} are predefined, as directory path and name of inventory file itself (without extension *.cfg)

    • more macro can be defined in "aliases" section

    • there is special construction split() in "aliases" section that allows to split alias ${NAME} to series of other aliases

    • this logic allows us to have just the same content of inventory files for all datasets, and vary only names of inventory files

Example of inventory file

{
   "aliases": {
       "CASE,PLATFORM,PROJECT": "split('${NAME}', '_')"
   },
   "name": "${NAME}",
   "case": "${CASE}",
   "assembly": "GRCh37",
   "platform": "${PLATFORM}",
   "config": "${DIR}/config.json",
   "fam": "${DIR}/${CASE}.fam",
   "patient-ids": "${DIR}/samples-${CASE}.csv",
   "vcf": "${DIR}/${NAME}.vcf",
   "vep-json": "${DIR}/${NAME}.vep.json",
   "anno-log": "${DIR}/annotations-${TS}.log",
   "a-json": "${DIR}/${CASE}_anfisa.json.gz",
   "docs": [
       {
           "source": "${DIR}/docs/notes.html",
           "kind": "html",
           "title": "Anamnesis"
       },
       {
           "source": "${DIR}/docs/pedigree.png",
                   "kind": "png",
           "dest": "pedigree.html",
                   "title": "Pedigree"

       },
       {
           "source": "${DIR}/docs/fulldoc.html",
           "kind": "html",
           "title": "Full documentation"
       }
   ]
}

Documentation block of inventory file

Property docs of inventory descriptor is list of objects that represent documentation items.

Common properties of documentation items:

• "kind" - kind of item, see details below

• "title" - title of item visible for the user

• "source" - path to location of file/files corresponding to the item, can contain template control symbols *, for some item kinds should match only one file

• "dest" - destination filename, for some item kinds is optional, in these cases base filename of source is used

Common rule: if there is no file / directory that is defined by "source" property, the documentation item is just ignored.

Kinds of documentation items

• kind = "group"

  Represents group (folder) of documentation items located in subdirectory. Descriptor should contain property "docs" with recursive list of sub-items of variour kinds. It is not recommended to define "dest" property explicitly.

• kind = "html"

  Represents document in HTML format. (Use "support" documentation item to use images inside document, see below). "source" should define a single document with .html extension. It is not recommended to define "dest" property explicitly.

• kind = "txt", kind = "png", kind = "jpg"

  Represents HTML document visible for the user with contents of file of text or image format. "source" should define a single document with corresponding extension. "dest" property should be explicitly defined as a filename with .html extension

  For image files the additional property "tooltip" can be used, with text description of the image

• kind = "*.txt", kind = "*.png", kind = "*.jpg"

  Represents single HTML document with contents of serie of files. "source" should define this serie. "dest" property should be explicitly defined as a filename with .html extension

• kind = "support"

  Represents subdirectory with supplementaty images. These images can be referenced inside HTML-documents and are invisible for the user on documentation tree. For this special kind of documentation item only "kind" and "source" properties should be defined, and "source" should be path to a subdirectory

See also

Administration file formats reference