Configuration files

Configuration files#

YAML-based config files in a project, folder, or stage serve as a single point of truth for all input files, output files or parameters. For this purpose, configurations can be defined at each level of your project in a params.in.yaml file. Using dso compile-config the params.in.yaml files are compiled into params.yaml with the following features:

  • inheritance: All variables defined in params.in.yaml files in any parent directory will be included.

  • templating: Variables can be composed using jinja2 syntax, e.g. foo: "{{ bar }}_version2".

  • path resolving: Paths will be always relative to each compiled params.yaml file, no matter where they were defined.

Therefore, you only need to read in a single params.yaml file in each stage.

Compiling configuration files#

To generate a params.yaml file for each params.in.yaml file, use:

dso compile-config

params.yaml files are not tracked by git. Never modify a params.yaml file by hand, it will be overwritten. In folders without a params.in.yaml file, no params.yaml file will be generated.

Inheritance#

The following diagram displays the inheritance of configurations:

../_images/dso-yaml-inherit.png

DSO leverages hiyapyco with method=METHOD_MERGE and none_behavior=NONE_BEHAVIOR_OVERRIDE to implement inheritance. This means

  • Values in a params.in.yaml file at a deeper level (e.g. stage) take precedence over values in a parent folder.

  • Values are added existing lists

  • Dictionary entried are added to existing dictionaries

  • To exclude an inherited parameter, set the variable to null.

Templating#

Templating is again implemented in hiyapyco using the interpolate=True flag. This allows variable to be composed using jinja2 syntax, e.g. foo: "{{ bar }}_version2".

Defining paths#

To ensure that, despite inheritance, paths are always relative to each compiled params.yaml file, relative paths need to be preceded with !path, e.g.:

samplesheet: !path "01_preprocessing/input/samplesheet.txt"

DSO supports compiling paths into absolute and relative paths. Relative paths are relative to the location of each compiled params.yaml file. By default, DSO uses relative paths. To enable absolute paths, see configuration. To learn how to work with relative paths in Python/R scripts see python usage and R usage.

Example#

Let’s consider a project which has the following two params.in.yaml files at the project root and in a stage subfolder.

/params.in.yaml
thresholds:
    fc: 2
    p_value: 0.05

metadata_file: !path "metadata/metadata.csv"
dataset_name: typical_analysis
file_with_abs_path: "/data/home/user/{{ dataset_name }}_data_set.csv"

remove_outliers: true

exclude_samples:
    - sample_1
    - sample_6
/stage/params.in.yaml
thresholds:
    fc: 3
    p_adjusted: 0.1

samplesheet: !path "01_preprocessing/input/samplesheet.txt"

remove_outliers: null

exclude_samples:
    - sample_42

This results in the following compiled params.yaml files:

/params.yaml
thresholds:
    fc: 2
    p_value: 0.05

metadata_file: metadata/metadata.csv
dataset_name: typical_analysis
file_with_abs_path: /data/home/user/typical_analysis_data_set.csv

remove_outliers: true

exclude_samples:
    - sample_1
    - sample_6
/stage/params.yaml
thresholds:
    fc: 3
    p_value: 0.05
    p_adjusted: 0.1

metadata_file: ../metadata/metadata.csv
dataset_name: typical_analysis
file_with_abs_path: /data/home/user/typical_analysis_data_set.csv

remove_outliers:

exclude_samples:
    - sample_1
    - sample_6
    - sample_42
samplesheet: 01_preprocessing/input/samplesheet.txt

Accessing stage config#

To ensure that dso correctly reruns stages when dependencies have changed, it is really important to declare all input files/params in dvc.yaml. dso compile-config generates params.yaml files that, in principle, you can read in with a YAML parser in a programming language of your choice. However, we recommend that you use one of the following interfaces to access the stage configuration. These interfaces ensure that you will have access only to the parameters declared in the dvc.yaml file as either input, parameter, or output. This ensure that you cannot forget to declare a parameter that you actually use in your analysis.

  • read_params in R

  • read_params in Python

  • dso get-config from the terminal.

dso get-config prints the filtered params file for a given stage to STDOUT. This makes it really easy to call it from other languages as a system call. In fact, this is what read_params in R and Python are doing under the hood.

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