Pipeline logo

render_logo.py generates logos for Sanger Tree of Life pipelines. Logos use the same layout as the nf-core logos, but customised to follow Sanger branding guidelines (Roboto font, specific shades of blue).

In Tree of Life, the script is already installed at /software/treeoflife/bin/render_logo.py, and its runtime dependencies are already available. There is nothing to install.

Quick start

In most cases you only need to point the script at the pipeline directory that contains .nf-core.yml:

/software/treeoflife/bin/render_logo.py --pipeline-dir /path/to/pipeline

This command:

• reads template.org and template.name from /path/to/pipeline/.nf-core.yml
• writes output files under /path/to/pipeline/docs/images/
• generates both dark and light variants
• prints the paths of the generated files on success

By default the output filenames are:

• /path/to/pipeline/docs/images/<org>-<name>_logo_dark.svg
• /path/to/pipeline/docs/images/<org>-<name>_logo_dark.png
• /path/to/pipeline/docs/images/<org>-<name>_logo_light.svg
• /path/to/pipeline/docs/images/<org>-<name>_logo_light.png

If you are already in the pipeline directory, this is equivalent:

/software/treeoflife/bin/render_logo.py --pipeline-dir .
# or
/software/treeoflife/bin/render_logo.py

If .nf-core.yml is missing or you want to override its values, supply the name as the positional argument, e.g. --org:

/software/treeoflife/bin/render_logo.py my-pipeline \
  --org sanger-tol \
  --pipeline-dir /path/to/pipeline

How the script works

The script uses the bundled sanger-tol.template.svg file as the geometry and style source. It updates the placeholder text, applies the appropriate text colour for each output mode, and then exports both SVG and PNG versions.

The output size is controlled by --height, which defaults to 4cm. Width is calculated automatically to preserve the aspect ratio. If the replacement name is wider than the placeholder in the template, the script increases the SVG canvas width just enough to keep the text clear of the embedded image while preserving the original right-hand padding.

To estimate how wide the new name will be, the script measures rendered text via Inkscape and Pillow. On the standard Tree of Life installation this should be fully available already. If rendered measurement fails for any reason, the script falls back to a simple width estimate so that logo generation can still continue.

Two path rules are worth knowing:

• --config and --output-dir are resolved relative to --pipeline-dir
• --template is resolved as given and is not automatically rebased onto --pipeline-dir

Common variations

Generate only the light logo:

/software/treeoflife/bin/render_logo.py --pipeline-dir /path/to/pipeline --mode light

Write output somewhere other than docs/images within the pipeline directory:

/software/treeoflife/bin/render_logo.py \
  --pipeline-dir /path/to/pipeline \
  --output-dir assets/logo

Run on your laptop with your own Inkscape installation (assumes you are in an environment with all dependencies installed, cf requirements.txt).

python3 /path/to/sanger-tol/nf-core-modules/scripts/logo/render_logo.py \
  --pipeline-dir /path/to/pipeline \
  --inkscape /path/to/Applications/Inkscape.app/Contents/MacOS/inkscape

Use a different metadata file under the same pipeline directory:

/software/treeoflife/bin/render_logo.py \
  --pipeline-dir /path/to/pipeline \
  --config config/custom.nf-core.yml

Use an explicit template file:

/software/treeoflife/bin/render_logo.py \
  --pipeline-dir /path/to/pipeline \
  --template /path/to/custom-template.svg

Complete usage

usage: render_logo.py [-h] [--org ORG] [--pipeline-dir PIPELINE_DIR]
                      [--config CONFIG] [--template TEMPLATE]
                      [--output-dir OUTPUT_DIR] [--mode {dark,light,all}]
                      [--height HEIGHT] [--inkscape INKSCAPE]
                      [name]

Positional argument

• name: Replacement text for the project label. If omitted, the script uses template.name from the selected .nf-core.yml file.

Options

• -h, --help: Show the built-in command help and exit.
• --org ORG: Organisation used in the output filename prefix. If omitted, the script uses template.org from the selected .nf-core.yml file.
• --pipeline-dir PIPELINE_DIR: Pipeline directory used as the base for resolving --config and --output-dir. Defaults to the current directory.
• --config CONFIG: Path to the metadata file used to discover template.org and template.name. Defaults to .nf-core.yml, resolved relative to --pipeline-dir.
• --template TEMPLATE: Path to the SVG template file. Defaults to the bundled sanger-tol.template.svg next to the script.
• --output-dir OUTPUT_DIR: Directory for generated SVG and PNG files. Defaults to docs/images, resolved relative to --pipeline-dir.
• --mode {dark,light,all}: Select which colour variant to generate. The default is all, which writes both dark and light outputs.
• --height HEIGHT: Output height written into the SVG, for example 4cm or 120px. Width is calculated automatically to preserve aspect ratio.
• --inkscape INKSCAPE: Command or full path for the Inkscape executable used for PNG export and text measurement. On Tree of Life systems the default inkscape should already work.

Behaviour and validation details

• The script requires a non-empty project name and organisation. You can supply them through .nf-core.yml, through the command line, or by combining both.
• If the selected config file does not exist, you must provide both name and --org on the command line.
• The script refuses empty values such as --org "".
• The script checks that the template file exists before rendering.
• The script checks that the requested Inkscape executable can be found on PATH unless you provide an explicit full path.
• The script creates the output directory if it does not already exist.
• On success it prints one output path per line.