Skip to content

MG-TK v0.69

Pre-release
Pre-release

Choose a tag to compare

View all tags
@willboulton willboulton released this 11 Nov 12:05
· 2 commits to main since this release
v0.69
595ab5c
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode. 
1st release version (MG-TK version 0.69)

* added the logo to repo

* Update README.md to use the logo

* QC report for MGTK using Kasia's and Rui's R scripts (#6)

* scripts to autogenerate a QC report

* changes to existing files to create the QC report

* remove hardcoded path in QC_html_report.Rmd

* Remove hardcoded path in QC_html_report.Rmd

* The actual call was commented out in MG-TK.pl

* bugs anthony noticed - coerce char type to num, some report looks weird

* GTDBtk v2.5 (#7)

* Get gtdb mash fix (#8)

* GTDBtk v2.5

* remove mash, don't install tk default

* fix(get_gtdb.py): remove mash for new versions, fix DBDir iterpolation, remove default GTDB-Tk install

Newer versions of GTDB-Tk (>=2.5) do not use mash, so when configuring for this, comments out the GTDBtk_mash line in config_DBs.txt

[DBDir] is now appropriately used in config, was previously not detected due to a newline character.

No longer install GTDB-Tk by default, allow MG-TK to install based on environment yamls. Added --install-tk flag to install a version of GTDB-Tk which is compataible with the GTDB released being configured.

---------

Co-authored-by: Falk Hildebrand <falk.hildebrand@gmail.com>

* Wb make qc report (#9)

* scripts to autogenerate a QC report

* changes to existing files to create the QC report

* remove hardcoded path in QC_html_report.Rmd

* Remove hardcoded path in QC_html_report.Rmd

* The actual call was commented out in MG-TK.pl

* bugs anthony noticed - coerce char type to num, some report looks weird

* installer changes, more reliably installs packages now

* trigger for creating html report

* MF -> MG-TK in documentation

* Update documentation MF -> MG-TK

* GTDBtk v2.5 (#10)

Co-authored-by: Falk Hildebrand <falk.hildebrand@gmail.com>

* funct assign prep

* fixed syntax error in curly brackets

* MGTKv0.69: cons call on the fly during gene cat to save space

* auto remove empty vcfs

* auto remove empty vcfs

* Update FAQ

Added new FAQ entries regarding MAG extraction and installation errors.

* make QC reporting quieter

---------

Co-authored-by: Will Boulton (QI) <rel25vaz@software23.hpccluster>
Co-authored-by: Anthony Duncan <36088426+apduncan@users.noreply.github.com>
Co-authored-by: Falk Hildebrand <falk.hildebrand@gmail.com>
Co-authored-by: Falk Hildebrand <falk.hildebrand@googlemail.com>
Assets 2
Loading