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Main config

Document generated: 2024-09-27 15:32:20 UTC+0000

Source: vignettes/config_main.Rmd
config_main.Rmd

Main config is stored in the config/single_sample/main.yaml and config/integration/main.yaml files (the location of this file is different for the single-sample and integration pipelines). As for the pipeline config, directory with this file is read from environment variables:

  • SCDRAKE_SINGLE_SAMPLE_CONFIG_DIR for the single-sample pipeline.
  • SCDRAKE_INTEGRATION_CONFIG_DIR for the integration pipeline.

Options named in lowercase are set upon scdrake load or attach. Then the actual directory used depends on whether you run run_single_sample_r() or run_integration_r().

Parameters in this config are used throughout all other stages. There are parameters such as project name, path to CSS file used to style HTML documents, or path to base output directory.

Project information 

PROJECT_NAME: "PBMC 1k"
PROJECT_DESCRIPTION: "1000 of peripheral blood mononuclear cells by 10x Genomics"
INSTITUTE: "Example institute"
LABORATORY: "Example laboratory"
PEOPLE: "Example person 1, Example person 2"

Type: character scalar

These values will appear in stage reports (HTML documents).

Annotation 

ORGANISM: "human"

Type: character scalar

A name of organism to match in ANNOTATION_LIST.

ANNOTATION_LIST:
  human: "org.Hs.eg.db"
  mouse: "org.Mm.eg.db"

Type: named list (dictionary) of character scalars

Mapping of organisms to OrgDb annotation packages. The annotation package is selected by matching the ORGANISM parameter. If the selected package is not installed, you will be asked if you want to install it.

In the OrgDb list you can find annotations for many other species, e.g. rat. The consequent modification of the config is simple:

ORGANISM: "rat"
ANNOTATION_LIST:
  rat: "org.Rn.eg.db"
ENSEMBL_SPECIES: "Homo_sapiens"

Type: character scalar

An ENSEMBL species name used to build links to Ensembl genes website, e.g. https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32315086-32400268

A list of ENSEMBL species is available at https://www.ensembl.org/info/about/species.html.

Input and output files 

CSS_FILE: "Rmd/common/stylesheet.css"

Type: character scalar

A path to CSS file used for HTML reports rendered from RMarkdown files.

BASE_OUT_DIR: "output"

Type: character scalar

A path to base output directory to which each stage’s files will be saved (check “Output files” section in stage configs).

Targets

An informative plan is binded with every other plan, and contains targets with useful runtime information:

config_pipeline, config_main: lists holding pipeline (pipeline.yaml) and main (00_main.yaml) parameters.

pipeline_type: a character scalar: "single_sample" or "integration". These values are used in some plans to work with different targets.

sessioninfo_pretty, sessioninfo_base: info about loaded packages, R version, etc. Returned from sessioninfo::session_info() and utils::sessionInfo(), respectively.

biocmanager_version: Bioconductor version.

external_libs: a character vector of external shared libraries (e.g. zlib).

datetime: date and time of pipeline execution.