diff --git a/CHANGELOG.md b/CHANGELOG.md index 427594d4e9..bbc618e9e8 100755 --- 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 @@ -35,15 +35,23 @@ - [**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** @@ -51,6 +59,9 @@ - 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 index 51e6142eef..509f58529d 100755 --- 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(