Changelog

MIPTools (development version)

When running the wrangler app, if the number of UMIs detected for a MIP is above a certain threshold, we reduce the UMI count to a lower value. This is done in order to increase the speed of our pipeline. Above a certain UMI count, the information becomes redundant (@arisp99, #40).
Add an additional argument to the wrangler app to control the population clustering fraction cutoff defined by MIPWrangler (@arisp99, #39).
Add the capability to freeze software version numbers when building the container. Additionally, the version number for key software tools has been fixed (@arisp99, #32).
Install mipscripts, which contains additional tools for analysis pipelines.
Perform additional argument parsing to ensure arguments are formatted correctly (#28, #37).
New download app supersedes the previous download app, which has been renamed to download_superseded. The new app improves the method for downloading data from the Illumina BaseSpace Sequence Hub by using the official command line tool (@arisp99, #25, #13).

Upgrade C and C++ compiler versions (#43).
Don’t install conda and mamba packages using defaults as this can cause the install process to hang.
Upgrade libgfortran4 to libgfortran5 (#38).
Let Freebayes run with only one CPU thread (#33).
Fix error when app arguments have whitespace characters (#26, #37).
Fix missing file error when MIP arms file is created from the MIP info dictionary (@aydemiro, #23).
Improve sample sheet preparation. Avoid errors when sample file columns are empty. Throw an error if there are invalid samples or input fields (@aydemiro, #22).
Fix build failure due to dependency changes in the McCOILR R package (#7).

Remove the msa2vcf program and other conversion tools (#35).
Reduce size of image by deleting source code after installation of programs.
Remove sequence aligners (#35).
Remove unused analysis settings files (#35).
Install programs from GitHub instead of storing source code (@arisp99, #36).
Update LICENSE year.
Store containers using an HTTP directory (#12).
Remove duplicated files.
Improve bash errors.
Make strings human readable (@arisp99, #5).

Add guides on probe design, data analysis, and HPCC use.
Generate online documentation using Sphinx and Github Pages.
Improve app documentation.
Add doc-strings to python functions.
Improve clarity of README and add additional instructions on downloading or building the container.