All the changelogs

changelog/multiqc/v0.1.mdx

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+---
+title: MultiQC v0.1
+date: 2015-09-01
+tags: [multiqc]
+---
+
+The first public release of MultiQC, after a month of development. Basic structure in place and modules for FastQC, FastQ Screen, Cutadapt, Bismark, STAR, Bowtie, Subread featureCounts and Picard MarkDuplicates. Approaching stability, though still under fairly heavy development.
+
+Download `MultiQC.app.zip` for the Mac OS X graphical tool. To run from the command line, download the zip of the code. Can also be installed directly with `pip` from [PyPI](https://pypi.python.org/pypi/multiqc/0.1):
+
+```
+pip install multiqc
+```

changelog/multiqc/v0.2.mdx

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+---
+title: MultiQC v0.2
+date: 2015-09-18
+tags: [multiqc]
+---
+
+A major rewrite of MultiQC, with a lot of stabilisation and sanitisation. Many new functions created in Python and JavaScript to handle common functions, making writing new modules much easier. New toolbox of features created for report, making it much more interactive.
+
+Download `MultiQC_v0.2.app.zip` for the Mac OS X graphical tool. To run from the command line, download the zip of the code. Can also be installed directly with `pip` from [PyPI](https://pypi.python.org/pypi/multiqc/0.1):
+
+```
+pip install multiqc
+```

changelog/multiqc/v0.3.1.mdx

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+---
+title: MultiQC v0.3.1
+date: 2015-11-04
+tags: [multiqc]
+---
+
+Hotfix to patch a bug that I found immediately after submitting v0.3.0 - sorry! Took the opportunity to add a few more new things to sweeten the deal.
+
+### Changelog
+- Hotfix patch to fix broken FastQC module (wasn't finding `.zip` files properly)
+- General Stats table colours now flat. Should improve browser speed.
+- Empty rows now hidden if appear due to column removal in general stats
+- FastQC Kmer plot removed until we have something better to show.

changelog/multiqc/v0.3.2.mdx

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+---
+title: MultiQC v0.3.2
+date: 2016-02-08
+tags: [multiqc]
+---
+
+New version - a number of new modules, a few new command line options and some new toys in the report user interface.
+
+I've just noticed that this was a bugfix version number bump and it should have been a minor version bump (`v0.4`). But I've already pushed this to PyPI so I'm not going to change it now. Sorry.
+
+Anyway, here's what's new:
+
+## Changelog
+- All modules now load their log file search parameters from a config
+  file, allowing you to overwrite them using your user config file
+  - This is useful if your analysis pipeline renames program outputs
+- New Picard (sub)modules - Insert Size, GC Bias & HsMetrics
+- New Qualimap (sub)module - RNA-Seq QC
+- Made Picard MarkDups show percent by default instead of counts
+- Added M-Bias plot to Bismark
+- New option to stream report HTML to `stdout`
+- Files can now be specified as well as directories
+- New options to specify whether the parsed data directory should be created
+  - command line flags: `--data` / `--no-data`
+  - config option name: `make_data_dir`
+- Fixed bug with incorrect path to installation dir config YAML file
+- New toolbox drawer for bulk-exporting graph images
+- Report side navigation can now be hidden to maximise horizontal space
+- Mobile styling improved for narrow screen
+- More vibrant colours in the general stats table
+- General stats table numbers now left aligned
+- Settings now saved and loaded to named localstorage locations
+  - Simplified interface - no longer global / single report saving
+  - Removed static file config. Solves JS error, no-one was doing this
+    since we have standalone reports anyway.
+- Added support for Python 3.5
+- Fixed bug with module specific CSS / JS includes in some templates
+- Made the 'ignore files' config use unix style file pattern matching
+- Fixed some bugs in the FastQ Screen module
+- Fixed some bugs in the FastQC module
+- Fixed occasional general stats table bug
+- Table sorting on sample names now works after renaming
+- Bismark module restructure
+  - Each report type now handled independently (alignment / dedup / meth extraction)
+  - M-Bias plot now shows R1 and R2
+- FastQC GC content plot now has option for counts or percentages
+  - Allows comparison between samples with very different read counts
+- Bugfix for reports javascript
+  - Caused by updated to remotely loaded HighCharts export script
+  - Export script now bundled with multiqc, so does not depend on internet connection
+  - Other JS errors fixed in this work
+- Bugfix for older FastQC reports - handle old style sequence dup data
+- Bugfix for varying Tophat alignment report formats
+- Bugfix for Qualimap RNA Seq reports with paired end data

changelog/multiqc/v0.3.mdx

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+---
+title: MultiQC v0.3
+date: 2015-11-04
+tags: [multiqc]
+---
+
+Lots of spit and polish added to MultiQC in this release - everything should now be properly documented and reports are quite a bit more stable.
+
+### Changelog
+- Lots of lovely new documentation!
+- Child templates - easily customise specific parts of the default report template
+- Plugin hooks - allow other tools to execute custom code during MultiQC execution
+- New Preseq module
+- New design for general statistics table (snazzy new background bars)
+- Further development of toolbox
+  - New button to clear all filters
+  - Warnings when samples are hidden, plus empty plots and table cols are hidden
+  - Active toolbar tab buttons are highlighted
+- Lots of refactoring by @moonso to please the Pythonic gods
+  - Switched to click instead of argparse to handle command line arguments
+  - Code generally conforms to best practices better now.
+- Now able to supply multiple directories to search for reports
+- Logging output improved (now controlled by `-q` and `-v` for quiet and verbose)
+- More HTML output dealt with by the base module, less left to the modules
+  - Module introduction text
+  - General statistics table now much easier to add to (new helper functions)
+- Images, CSS and Javascript now included in HTML, meaning that there is a single
+  report file to make sharing easier
+- More accessible scrolling in the report - styled scrollbars and 'to top' button.
+- Modules and templates now use setuptools entry points, facilitating plugins
+  by other packages. Allows niche extensions whilst keeping the core codebase clean.
+- The general stats table now has a sticky header row when scrolling, thanks to
+  some new javascript wizardry...
+- General stats columns can have a _shared key_ which allows common colour schemes
+  and data ranges. For instance, all columns describing a read count will now share
+  their scale across modules.
+- General stats columns can be hidden and reordered with a new modal window.
+- Plotting code refactored, reports with many samples (>50 by default) don't
+  automatically render to avoid freezing the browser.
+- Plots with highlighted and renamed samples now honour this when exporting to
+  different file types.

changelog/multiqc/v0.4.mdx

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+---
+title: MultiQC v0.4
+date: 2016-02-16
+tags: [multiqc]
+---
+
+Latest release of MultiQC with some tasty new functions..
+- New `multiqc_sources.txt` which identifies the paths used to collect all report data for each sample
+- Export parsed data as tab-delimited text, `JSON` or `YAML` using the new `-k`/`--data-format` command line option
+- Updated HighCharts from `v4.2.2` to `v4.2.3`, fixes tooltip hover bug.
+- Nicer export button. Now tied to the export toolbox, hopefully more intuitive.
+- FastQC: Per base sequence content heatmap can now be clicked to show line graph for single sample
+- FastQC: No longer show adapter contamination datasets with &lte; 0.1% contamination.
+- Picard: Added support for `CollectOxoGMetrics` reports.
+- Changed command line option `--name` to `--filename`
+- `--name` also used for filename if `--filename` not specified.
+- Hide samples toolbox now has switch to _show only_ matching samples
+- New regex help box with examples added to report
+- New button to copy general stats table to the clipboard
+- General Stats table 'floating' header now sorts properly when scrolling
+- Bugfix: MultiQC default_dev template now copies module assets properly
+- Bufgix: General Stats table floating header now resizes properly when page width changes

changelog/multiqc/v0.5.mdx

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+---
+title: MultiQC v0.5
+date: 2016-03-29
+tags: [multiqc]
+---
+
+Latest version of MultiQC. Key highlights are **big reports** (hundreds / thousands of samples now possible), numerous **new modules**, better **plugin framework** and a bunch of tweaks for smoother running.
+
+Changelog:
+- New [Skewer](https://github.com/relipmoc/skewer) module, written by @dakl
+- New [Samblaster](https://github.com/GregoryFaust/samblaster) module, written by @dakl
+- New [Samtools stats](http://www.htslib.org/) module, written by @lpantano
+- New [HiCUP](http://www.bioinformatics.babraham.ac.uk/projects/hicup/) module
+- New [SnpEff](http://snpeff.sourceforge.net/) module
+- New [methylQA](http://methylqa.sourceforge.net/) module
+- New "Flat" image plots, rendered at run time with MatPlotLib
+  - By default, will use image plots if > 50 samples (set in config as `plots_flat_numseries`)
+  - Means that _very_ large numbers of samples can be viewed in reports. _eg._ single cell data.
+  - Templates can now specify their own plotting functions
+  - Use `--flat` and `--interactive` to override this behaviour
+- MultiQC added to `bioconda` (with help from @dakl)
+- New plugin hook: `config_loaded`
+- Plugins can now add new command line options (thanks to @robinandeer)
+- Changed default data directory name from `multiqc_report_data` to `multiqc_data`
+- Removed support for depreciated MultiQC_OSXApp
+- Updated logging so that a verbose `multiqc_data/.multiqc.log` file is always written
+- Now logs more stuff in verbose mode - command used, user configs and so on.
+- Added a call to multiqc.info to check for new versions. Disable with config `no_version_check`
+- Removed general stats manual row sorting.
+- Made filename matching use glob unix style filename match patterns
+- Everything (including the data directory) is now created in a temporary directory and moved when MultiQC is complete.
+- A handful of performance updates for large analysis directories

changelog/multiqc/v0.6.mdx

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+---
+title: MultiQC v0.6
+date: 2016-04-29
+tags: [multiqc]
+---
+
+Date released: 2016-04-29
+
+Key highlights in this report are **new plot types**! Beeswarm and generalised tables. **Three new modules**, a major internal **code refactoring** around plotting and tables (now easier to understand, maintain and add to) and a whole swath of other minor module updates, new functions and features..
+
+Changelog:
+- New [Salmon](http://combine-lab.github.io/salmon/) module.
+- New [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) module.
+- New [Bamtools stats](https://github.com/pezmaster31/bamtools) module.
+- New beeswarm plot type. General Stats table replaced with this when many samples in report.
+- New RSeQC module: Actually a suite of 8 new modules supporting various outputs from RSeQC
+- Rewrote bowtie2 module: Now better at parsing logs and tries to scrape input from wrapper logs.
+- Made cutadapt show counts by default instead of obs/exp
+- Dynamic plots now update their labels properly when changing datasets and to percentages
+- Config files now loaded from working directory if present
+- Started new docs describing how each module works
+- Refactored featureCounts module. Now handles summaries describing multiple samples.
+- Stopped using so many hidden files. `.multiqc.log` now called `multiqc.log`
+- New `-c`/`--config` command line option to specify a MultiQC configuration file
+- Can now load run-specific config files called `multiqc_config.yaml` in working directory
+- Large code refactoring - moved plotting code out of `BaseModule` and into new `multiqc.plots` submodules
+- Generalised code used to generate the General Stats table so that it can be used by modules
+- Removed interactive report tour, replaced with a link to a youtube tutorial
+- Made it possible to permanently hide the blue welcome message for all future reports
+- New option to smooth data for line plots. Avoids mega-huge plots. Applied to SnpEff, RSeQC, Picard.
+- Added percentage view to Picard insert size plot
+- Bugfix: Qualimap handles infinity symbol (thanks @chapmanb )
+- Bugfix: Made SnpEff less fussy about required fields for making plots
+- Bufgix: UTF-8 file paths handled properly in Py2.7+
+- Bugfix: Extending two config variables wasn't working. Now fixed.
+- Bugfix: Dragging the height bar of plots now works again.
+- Bugfix: Plots now properly change y axis limits and labels when changing datasets
+- Bugfix: Flat plots now have correct path in `default_dev` template

changelog/multiqc/v0.7.mdx

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+---
+title: MultiQC v0.7
+date: 2016-07-04
+tags: [multiqc]
+---
+
+## Version 0.7 of MultiQC!
+
+This is quite a big release: 141 commits since v0.6, with 4,587 new lines of code and 2,116 lines deleted (or updated), affecting 75 files. Many thanks to everyone for your patience.
+
+### MultiQC is published!
+
+If you didn't hear about it - the reason that I wanted to keep the main release stable was because the MultiQC paper was under review. It went well, and MultiQC is now published! You can see it here:
+
+> **MultiQC: Summarize analysis results for multiple tools and samples in a single report**
+> _Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller_
+> Bioinformatics (2016)
+> doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354)
+> PMID: [27312411](http://www.ncbi.nlm.nih.gov/pubmed/27312411)
+
+Many thanks to everyone involved.
+
+### Module updates:
+
+Not a huge number of new modules this time, but lots of fixed bugs and quite a few big extensions / refactoring of big modules.
+- [**Kallisto**](https://pachterlab.github.io/kallisto/) - new module!
+- **Picard**
+  - Code refactored to make maintenance and additions easier.
+  - Big update to `HsMetrics` parsing - more results shown in report, new plots (by @lpantano)
+  - Updated `InsertSizeMetrics` to understand logs generated by `CollectMultipleMetrics` (#215)
+  - Newlines in picard output. Fixed by @dakl
+- **Samtools**
+  - Code refactored
+  - Rewrote the `samtools stats` code to display more stats in report with a beeswarm plot.
+- **Qualimap**
+  - Rewritten to use latest methods and fix bugs.
+  - Added _Percentage Aligned_ column to general stats for `BamQC` module.
+  - Extra table thresholds added by @avilella (hidden by default)
+- **General Statistics**
+  - Some tweaks to the display defaults (FastQC, Bismark, Qualimap, SnpEff)
+  - Now possible to skip the General Statistics section of the report with `--exclude general_stats`
+- **Cutadapt** module updated to recognise logs from old versions of cutadapt (&lte; v1.6)
+- **Trimmomatic**
+  - Now handles `,` decimal places in percentage values.
+  - Can cope with line breaks in log files (see issue #212)
+- **FastQC** refactored
+  - Now skips zip files if the sample name has already been found. Speeds up MultiQC execution.
+  - Code cleaned up. Parsing and data-structures standardised.
+  - New popovers on Pass / Warn / Fail status bars showing sample names. Fast highlighting and hiding.
+  - New column in General Stats (hidden by default) showing percentage of FastQC modules that failed.
+- **SnpEff**
+  - Search pattern now more generic, should match reports from others.
+  - _Counts by Effect_ plot removed (had hundreds of categories, was fairly unusable).
+  - `KeyError` bug fixed.
+- **Samblaster** now gets sample name from `ID` instead of `SM` (@dakl)
+- **Bowtie 2**
+  - Now parses overall alignment rate as intended.
+  - Now depends on even less log contents to work with more inputs.
+- **MethylQA** now handles variable spacing in logs
+- **featureCounts** now splits columns on tabs instead of whitespace, can handle filenames with spaces
+
+### Core updates:
+- **Galaxy**: MultiQC now available in Galaxy! Work by @devengineson / @yvanlebras / @cmonjeau
+  - See it in the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/view/engineson/multiqc/)
+- **Heatmap**: New plot type!
+- **Scatter Plot**: New plot type!
+- **Download raw data** behind plots in reports! Available in the Export toolbox.
+  - Choose from tab-separated, comma-separated and the complete JSON.
+- **Table columns can be hidden** on page load (shown through _Configure Columns_)
+  - Defaults are configurable using the `table_columns_visible` config option.
+- **Beeswarm plot**: Added missing rename / highlight / hiding functionality.
+- New `-l` / `--file-list` option: specify a file containing a **list of files** to search.
+- **Updated HighCharts** to v4.2.5. Added option to export to JPEG.
+- Can now **cancel execution** with a single `ctrl+c` rather than having to button mash
+- More granular control of **skipping files** during scan (filename, dirname, path matching)
+  - Fixed `--exclude` so that it works with directories as well as files
+- **New _Clear_ button** in toolbox to bulk remove highlighting / renaming / hiding filters.
+- Improved documentation about behaviour for large sample numbers.
+- Handle YAML parsing errors for the config file more gracefully
+- Removed empty columns from tables again
+- Fixed bug in changing module search patterns, reported by @lweasel
+- Added timeout parameter to version check to prevent hang on systems with long defaults
+- Fixed table display bug in Firefox
+- Fixed bug related to order in which config files are loaded
+- Fixed bug that broke the _"Show only"_ toolbox feature with multiple names.
+- Numerous other small bugs.