Published January 11, 2018
| Version v1.4
Software
Open
ewels/MultiQC: MultiQC Version 1.4
Creators
- Phil Ewels1
- Markus J. Ankenbrand2
- Rickard Hammarén
- Vlad Saveliev3
- Tim Booth4
- Aled Jones
- Tobias Neumann5
- Måns Magnusson6
- alexanderscholz
- Robin Andeer7
- Sacha Laurent
- Guillermo Carrasco8
- Winni Kretzschmar
- Francesco
- hxin
- Lorena Pantano9
- Matthias De Smet
- Remi-Andre Olsen
- Devon Ryan10
- Brad Chapman11
- Fredrik Boulund12
- Julian Gehring13
- Joachim Wolff14
- Heather L. Wiencko
- Murray Wham
- Maxime Garcia15
- Dennis Schwartz16
- Dimitri Desvillechabrol17
- Albert Vilella18
- Roman Valls Guimerà19
- 1. Science for Life Laboratory
- 2. University of Würzburg
- 3. @UMCCR
- 4. Edinburgh Genomics
- 5. @IMPIMBA @ZuberLab
- 6. Science for Life Labs
- 7. @Clinical-Genomics
- 8. @iZettle
- 9. Harvard Chan School of Public Health
- 10. Max Planck Institute of Immunobiology and Epigenetics
- 11. Harvard Chan Bioinformatics Core
- 12. Karolinska Institute
- 13. Illumina
- 14. @BackofenLab Albert-Ludwigs-University Freiburg im Breisgau
- 15. @SciLifeLab | Karolinska Institutet
- 16. Repositive.io
- 17. Institut Curie
- 18. @cegx
- 19. UMCCR
Description
A slightly earlier-than-expected release due to a new problem with dependency packages that is breaking MultiQC installations since 2018-01-11.
New Modules:- Sargasso
- Parses output from Sargasso - a tool to separate mixed-species RNA-seq reads according to their species of origin
- Module written by @hxin
- VerifyBAMID
- Parses output from VerifyBAMID - a tool to detect contamination in BAM files.
- Adds the
CHIPMIX
andFREEMIX
columns to the general statistics table. - Module written by @aledj2
- MACS2
- Updated to work with output from older versions of MACS2 by @avilella
- Peddy
- Add het check plot to suggest potential contamination by @aledj2
- Picard
- Picard HsMetrics
HS_PENALTY
plot now has correct axis labels - InsertSizeMetrics switches commas for points if it can't convert floats. Should help some european users.
- Picard HsMetrics
- QoRTs
- Added support for new style of output generated in the v1.3.0 release
- Qualimap
- QUAST
- New option to customise the default display of contig count and length (eg.
bp
instead ofMbp
). - See documentation. Written by @ewels and @Cashalow
- New option to customise the default display of contig count and length (eg.
- RSeQC
- Removed normalisation in Junction Saturation plot. Now raw counts instead of % of total junctions.
- Conditional formatting / highlighting of cell contents in tables
- If you want to make values that match a criteria stand out more, you can now write custom rules and formatting instructions for tables.
- For instructions, see the documentation
- New
--lint
option which is strict about best-practices for writing new modules- Useful when writing new modules and code as it throws warnings
- Currently only implemented for bar plots and a few other places. More linting coming soon...
- If MultiQC breaks and shows am error message, it now reports the filename of the last log it found
- Hopefully this will help with debugging / finding dodgy input data
- Addressed new dependency error with conflicting package requirements
- There was a conflict between the
networkx
,colormath
andspectra
releases. - I previously forced certain software versions to get around this, but
spectra
has now updated with the unfortunate effect of introducing a new dependency clash that halts installation.
- There was a conflict between the
- Fixed newly introduced bug where Custom Content MultiQC config file search patterns had been broken
- Updated pandoc command used in
--pdf
to work with new releases of Pandoc - Made config
table_columns_visible
module name key matching case insensitive to make less frustrating
Files
ewels/MultiQC-v1.4.zip
Files
(2.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/ewels/MultiQC/tree/v1.4 (URL)