Changelog

MIPTools (development version)

New Features

  • New features that have been introduced since the most recent release will appear here until they get rolled into the next release.

MIPTools 0.5.0

New Features

  • User can call a single script, run_miptools.sh, which automatically launches the other steps of miptools.

  • shell scripts and config files now have version numbers associated to reduce confusion around which sif files are compatible with which scripts. for interactively exploring mutation prevalences.

  • Added a choropleth map jupyter notebook, called prevalence_plotting.ipynb, for interactively exploring mutation prevalences.

  • Introduced a config.yaml file that eliminates the need for user to provide binding arguments to singularity

  • wrangling and variant calling are now both subdivided into snakemake steps so that partially completed jobs can be resumed and so that crashes report the exact step where a crash occurred. This also improves scalability to large datasets.

  • 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).

Bug Fixes

  • Removed an alarming (but ultimately harmless) error message associated with snakemake ‘shell’ commands.

  • Removed the redundant mip_info.json files so they’re no longer required by the pipeline.

  • Upgraded pandas to a newer version and fixed ambiguous merge commands

  • Upgraded jupyter notebooks to a newer version

  • Upgraded conda packages.

  • Added cached wrangler and conda sif files to avoid automatically rebuilding these on MIPTools rebuild.

  • 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).

Maintenance

  • 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).

Documentation Overhaul

  • 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.

MIPTools 0.4.0

  • Latest stable build.