Resource Update Guide

Purpose

This guide describes how to update tools and resources used by VIP.

Overview

Pipeline dependencies are divided into tools and resources.

Tools

Tools are software components packaged as Apptainer container images.

Examples

  • BCFtools
  • Minimap2
  • Mosdepth

Updates typically involve

  • Updating the .def file
  • Building a new .sif image
  • Uploading the .sif to registry
  • Updating the pipeline to use the new .sif
  • Validation

Resources

Resources are non-executable datasets or configuration assets used by tools during analysis.

Examples

  • ClinVar
  • HPO
  • Classification tree
  • Report template

Updates typically involve

  • Uploading the resources to registry
  • Updating the pipeline to use the new resource
  • Validation

Updating Tools

Decide whether this tool requires default or exceptional update procedure.

Default

  • Locate <tool>.def file in utils/apptainer/def
  • Update tool version number in the <tool>.def file
  • Update tool version number in the <tool>.def filename
  • Update tool version number in utils/apptainer/makefile
  • Run make <tool>
  • Ensure that filename was changed to prevent file overwrite in next step as well as prevent user caching issues
  • Upload sif/<tool_with_updated_filename>.sif to https://download.molgeniscloud.org/downloads/vip/images
  • Run md5sum sif/<tool_with_updated_filename>.sif
  • Update <tool_with_updated_filename>.sif filename and checksum in /install_data.sh located in function install_files()
  • Update <tool_with_updated_filename>.sif in config/nxf_<workflow>.config

Exceptions

Exceptional update procedure might exist for some tools, contact @bartcharbon or @dennishendriksen.

Updating Resources

Decide whether this resource requires default or exceptional update procedure.

Default

  • Ensure that resource filename was changed to prevent file overwrite in next step as well as prevent user caching issues
  • Upload <resource> to https://download.molgeniscloud.org/downloads/vip/resources or the relevant subfolder
  • Run md5sum <resource>
  • Update <resource> filename and checksum in /install_data.sh located in function install_files()
  • Update references to <resource> in pipeline code

Exceptions

Exceptional update procedure might exist for some tools, contact @bartcharbon or @dennishendriksen.