Bump to v1.12

Organise changelog into better sections for v1.12
MultiQC · Feb 8, 2022 · 4aede39 · 4aede39
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,30 +1,30 @@
 # MultiQC Version History
 
-## MultiQC v1.12dev
+## [MultiQC v1.12](https://github.com/ewels/MultiQC/releases/tag/v1.12) - 2022-02-08
 
-### MultiQC updates
+### MultiQC - new features
 
-- Fixed issue with format sambamba markdup 0.8.1 ([#1617](https://github.com/ewels/MultiQC/issues/1617))
 - Added option to customise default plot height in plot config ([#1432](https://github.com/ewels/MultiQC/issues/1432))
 - Added `--no-report` flag to skip report generation ([#1462](https://github.com/ewels/MultiQC/issues/1462))
 - Added support for priting tool DOI in report sections ([#1177](https://github.com/ewels/MultiQC/issues/1177))
-- Fixed logger bugs when calling `multiqc.run` multiple times by removing logging file handlers between calls ([#1141](https://github.com/ewels/MultiQC/issues/1141))
-- Added missing functions call to several modules ([#1468](https://github.com/ewels/MultiQC/issues/1468))
-- Wrote new script to check for core function calls that should be in every module (`.github/workflows/code_checks.py`), runs on GitHub actions CI
 - Added support for `--custom-css-file` / `config.custom_css_files` option to include custom CSS in the final report ([#1573](https://github.com/ewels/MultiQC/pull/1573))
+- New plot config option `labelSize` to customise font size for axis labels in flat MatPlotLib charts ([#1576](https://github.com/ewels/MultiQC/pull/1576))
+- Added support for customising table column names ([#1255](https://github.com/ewels/MultiQC/issues/1255))
+
+### MultiQC - updates
+
 - MultiQC now skips modules for which no files were found - gives a small performance boost ([#1463](https://github.com/ewels/MultiQC/issues/1463))
-- New option to customise font size for axis labels in flat MatPlotLib charts ([#1576](https://github.com/ewels/MultiQC/pull/1576))
-- CSS Improvements to make printed reports more attractive / readable ([#1579](https://github.com/ewels/MultiQC/pull/1579))
-- Always save `custom content` data to file with a name reflecting the section name. ([#1194](https://github.com/ewels/MultiQC/issues/1194))
-- Sort custom content bargraph data by default ([#1412](https://github.com/ewels/MultiQC/issues/1412))
+- Improvements for running MultiQC in a Python environment, such as a Jupyter Notebook or script
+  - Fixed logger bugs when calling `multiqc.run` multiple times by removing logging file handlers between calls ([#1141](https://github.com/ewels/MultiQC/issues/1141))
+  - Init/reset global state between runs ([#1596](https://github.com/ewels/MultiQC/pull/1596))
+- Added commonly missing functions to several modules ([#1468](https://github.com/ewels/MultiQC/issues/1468))
+- Wrote new script to check for the above function calls that should be in every module (`.github/workflows/code_checks.py`), runs on GitHub actions CI
 - Make table _Conditional Formatting_ work at table level as well as column level. ([#761](https://github.com/ewels/MultiQC/issues/761))
-- Added support for customising table column names ([#1255](https://github.com/ewels/MultiQC/issues/1255))
-- Init/reset global state between runs ([#1596](https://github.com/ewels/MultiQC/pull/1596))
+- CSS Improvements to make printed reports more attractive / readable ([#1579](https://github.com/ewels/MultiQC/pull/1579))
 - Fixed a problem with numeric filenames ([#1606](https://github.com/ewels/MultiQC/issues/1606))
 - Fixed nasty bug where line charts with a categorical x-axis would take categories from the last sample only ([#1568](https://github.com/ewels/MultiQC/issues/1568))
 - Ignore any files called `multiqc_data.json` ([#1598](https://github.com/ewels/MultiQC/issues/1598))
 - Check that the config `path_filters` is a list, convert to list if a string is supplied ([#1539](https://github.com/ewels/MultiQC/issues/1539))
-- Custom Content: Use filename for section header in files with no headers ([#1550](https://github.com/ewels/MultiQC/issues/1550))
 
 ### New Modules
 
@@ -35,22 +35,33 @@
 - [**WhatsHap**](https://whatshap.readthedocs.io)
   - WhatsHap is a software for phasing genomic variants using DNA sequencing reads
 
+### Module feature additions
+
+- **BBMap**
+  - Added handling for `qchist` output ([#1021](https://github.com/ewels/MultiQC/issues/1021))
+- **bcftools**
+  - Added a plot with samplewise number of sites, Ts/Tv, number of singletons and sequencing depth ([#1087](https://github.com/ewels/MultiQC/issues/1087))
+- **Mosdepth**
+  - Added mean coverage [#1566](https://github.com/ewels/MultiQC/issues/1566)
+- **NanoStat**
+  - Recognize FASTA and FastQ report flavors ([#1547](https://github.com/ewels/MultiQC/issues/1547))
+
 ### Module updates
 
 - **BBMap**
   - Correctly handle adapter stats files with additional columns ([#1556](https://github.com/ewels/MultiQC/issues/1556))
-  - Added handling for `qchist` output ([#1021](https://github.com/ewels/MultiQC/issues/1021))
 - **bclconvert**
   - Handle change in output format in v3.9.3 with new `Quality_Metrics.csv` file ([#1563](https://github.com/ewels/MultiQC/issues/1563))
-- **bcftools**
-  - Added a plot with samplewise number of sites, Ts/Tv, number of singletons and sequencing depth ([#1087](https://github.com/ewels/MultiQC/issues/1087))
 - **bowtie**
   - Minor update to handle new log wording in bowtie v1.3.0 ([#1615](https://github.com/ewels/MultiQC/issues/1615))
 - **CCS**
   - Tolerate compound IDs generated by pbcromwell ccs in the general statistics ([#1486](https://github.com/ewels/MultiQC/pull/1486))
   - Fix report parsing. Update test on attributes ids ([#1583](https://github.com/ewels/MultiQC/issues/1583))
 - **Custom content**
   - Fixed module failing when writing data to file if there is a `/` in the section name ([#1515](https://github.com/ewels/MultiQC/issues/1515))
+  - Use filename for section header in files with no headers ([#1550](https://github.com/ewels/MultiQC/issues/1550))
+  - Sort custom content bargraph data by default ([#1412](https://github.com/ewels/MultiQC/issues/1412))
+  - Always save `custom content` data to file with a name reflecting the section name. ([#1194](https://github.com/ewels/MultiQC/issues/1194))
 - **DRAGEN**
   - Fixed bug in sample name regular expression ([#1537](https://github.com/ewels/MultiQC/pull/1537))
 - **Fastp**
@@ -67,11 +78,8 @@
 - **miRTrace**
   - Replace hardcoded RGB colours with Hex to avoid errors with newer versions of matplotlib ([#1263](https://github.com/ewels/MultiQC/pull/1263))
 - **Mosdepth**
-  - Added mean coverage, as requested by [#1566](https://github.com/ewels/MultiQC/issues/1566)
   - Fixed issue [#1568](https://github.com/ewels/MultiQC/issues/1568)
   - Fixed a bug when reporting per contig coverage
-- **NanoStat**
-  - Recognize FASTA and FastQ report flavors ([#1547](https://github.com/ewels/MultiQC/issues/1547))
 - **Picard**
   - Update `ExtractIlluminaBarcodes` to recognise more log patterns in newer versions of Picard ([#1611](https://github.com/ewels/MultiQC/pull/1611))
 - **Qualimap**
@@ -83,6 +91,8 @@
   - Fixed bug in the `junction_saturation` submodule ([#1582](https://github.com/ewels/MultiQC/issues/1582))
   - Fixed bug where empty files caused `tin` submodule to crash ([#1604](https://github.com/ewels/MultiQC/issues/1604))
   - Fix bug in `read_distribution` for samples with zero tags ([#1571](https://github.com/ewels/MultiQC/issues/1571))
+- **Sambamba**
+  - Fixed issue with a change in the format of output from `sambamba markdup` 0.8.1 ([#1617](https://github.com/ewels/MultiQC/issues/1617))
 - **Skewer**
   - Fix `ZeroDivisionError` if no available reads are found ([#1622](https://github.com/ewels/MultiQC/issues/1622))
 - **Somalier**

diff --git a/setup.py b/setup.py
@@ -24,7 +24,7 @@
 from setuptools import setup, find_packages
 import sys
 
-version = "1.12dev"
+version = "1.12"
 dl_version = "master" if "dev" in version else "v{}".format(version)
 
 print(