Bump to v1.16 (#2067)

* Bump to v1.16

* Update release checklist

* Add instruction to release checklist to install MultiQC_NGI

.github/RELEASE_CHECKLIST.md

@@ -25,6 +25,20 @@ This checklist is for my own reference, as I forget the steps every time.
      mv ~/.multiqc_config.yml ~/.multiqc_config.yml.bkup
      ```
 
+   - Install `NationalGenomicsInfrastructure/MultiQC_NGI`:
+
+     ```bash
+     pip install git+https://github.com/NationalGenomicsInfrastructure/MultiQC_NGI@0.7.1
+     ```
+
+   - Generate reports in the multiqc/website repo.
+
+     ```bash
+     bash update_examples.sh
+     ```
+
+   - Put back homedir config
+
      ```bash
      mv ~/.multiqc_config.yml.bkup ~/.multiqc_config.yml
      ```

CHANGELOG.md

@@ -1,6 +1,6 @@
 # MultiQC Version History
 
-## MultiQC v1.16dev
+## [MultiQC v1.16](https://github.com/ewels/MultiQC/releases/tag/v1.16) - 2023-09-22
 
 ### Highlight: Software versions
 
@@ -25,7 +25,7 @@ This idea goes way back to [issue #290](https://github.com/ewels/MultiQC/issues/
 
 - Removed `simplejson` unused dependency ([#1973](https://github.com/ewels/MultiQC/pull/1973))
 - Give config `custom_plot_config` priority over column-specific settings set by modules
-- When exporting plots, make a more clear error message for unsupported FastQC dot plot [#1976](https://github.com/ewels/MultiQC/pull/1976)
+- When exporting plots, make a more clear error message for unsupported FastQC dot plot ([#1976](https://github.com/ewels/MultiQC/pull/1976))
 - Fixed parsing of `plot_type: "html"` `data` in json custom content
 - Replace deprecated `pkg_resources`
 - [Fix](https://github.com/ewels/MultiQC/issues/2032) the module groups configuration for modules where the namespace is passed explicitly to `general_stats_addcols`. Namespace is now always appended to the module name in the general stats ([2037](https://github.com/ewels/MultiQC/pull/2037)).
@@ -38,43 +38,42 @@ This idea goes way back to [issue #290](https://github.com/ewels/MultiQC/issues/
 
 - [**Bakta**](https://github.com/oschwengers/bakta)
   - Rapid and standardized annotation of bacterial genomes, MAGs & plasmids.
-- [mapDamage](https://github.com/ginolhac/mapDamage)
+- [**mapDamage**](https://github.com/ginolhac/mapDamage)
   - mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
 - [**Sourmash**](https://github.com/sourmash-bio/sourmash)
   - Quickly search, compare, and analyze genomic and metagenomic data sets.
 
 ### Module updates
 
+- **BcfTools**
+  - Stats: fix parsing multi-sample logs ([#2052](https://github.com/ewels/MultiQC/issues/2052))
 - **Custom content**
   - Don't convert sample IDs to floats ([#1883](https://github.com/ewels/MultiQC/issues/1883))
+- **DRAGEN**
+  - Make DRAGEN module use `fn_clean_exts` instead of hardcoded file names. Fixes working with arbitrary file names ([#1994](https://github.com/ewels/MultiQC/pull/1994))
+- **FastQC**:
+  - fix `UnicodeDecodeError` when parsing `fastqc_data.txt`: try latin-1 or fail gracefully ([#2024](https://github.com/ewels/MultiQC/issues/2024))
+- **Kaiju**:
+  - Fix `UnboundLocalError` on outputs when Kanju was run with the `-e` flag ([#2023](https://github.com/ewels/MultiQC/pull/2023))
 - **Kraken**
+  - Parametrize top-N through config ([#2060](https://github.com/ewels/MultiQC/pull/2060))
   - Fix bug where ranks incorrectly assigned to tabs ([#1766](https://github.com/ewels/MultiQC/issues/1766)).
 - **Mosdepth**
   - Add X/Y relative coverage plot, analogous to the one in samtools-idxstats ([#1978](https://github.com/ewels/MultiQC/issues/1978))
   - Added the `perchrom_fraction_cutoff` option into the config to help avoid clutter in contig-level plots
   - Fix a bug happening when both `region` and `global` coverage histograms for a sample are available (i.e. when mosdepth was run with `--by`, see [mosdepth docs](https://github.com/brentp/mosdepth#usage)). In this case, data was effectively merged. Instead, summarise it separately and add a separate report section for the region-based coverage data.
   - Do not fail when all input samples have no coverage ([#2005](https://github.com/ewels/MultiQC/pull/2005)).
-- **RSeQC**
-  - Fix "max() arg is an empty sequence" error ([#1985](https://github.com/ewels/MultiQC/issues/1985))
-  - Fix division by zero on all-zero input ([#2040](https://github.com/ewels/MultiQC/pull/2040))
 - **NanoStat**
   - Support new format ([#1997](https://github.com/ewels/MultiQC/pull/1997)).
-- **DRAGEN**
-  - Make DRAGEN module use `fn_clean_exts` instead of hardcoded file names. Fixes working with arbitrary file names ([#1994](https://github.com/ewels/MultiQC/pull/1994))
-- **WhatsHap**
-  - Bugfix: ensure that TSV is only split on tab character. Allows sample names with spaces ([#1981](https://github.com/ewels/MultiQC/pull/1981))
+- **RSeQC**
+  - Fix `max() arg is an empty sequence` error ([#1985](https://github.com/ewels/MultiQC/issues/1985))
+  - Fix division by zero on all-zero input ([#2040](https://github.com/ewels/MultiQC/pull/2040))
 - **Samtools**
   - Stats: fix "Percent Mapped" plot when samtools was run with read filtering ([#1972](https://github.com/ewels/MultiQC/pull/1972))
-- **FastQC**:
-  - fix `UnicodeDecodeError` when parsing `fastqc_data.txt`: try latin-1 or fail gracefully ([#2024](https://github.com/ewels/MultiQC/issues/2024))
-- **Kaiju**:
-  - Fix `UnboundLocalError` on outputs when Kanju was run with the `-e` flag ([#2023](https://github.com/ewels/MultiQC/pull/2023))
 - **Qualimap**
   - BamQC: Include `% On Target` in General Stats table ([#2019](https://github.com/ewels/MultiQC/issues/2019))
-- **BcfTools**
-  - Stats: fix parsing multi-sample logs ([#2052](https://github.com/ewels/MultiQC/issues/2052))
-- **Kraken**
-  - Parametrize top-N through config ([#2060](https://github.com/ewels/MultiQC/pull/2060))
+- **WhatsHap**
+  - Bugfix: ensure that TSV is only split on tab character. Allows sample names with spaces ([#1981](https://github.com/ewels/MultiQC/pull/1981))
 
 ## [MultiQC v1.15](https://github.com/ewels/MultiQC/releases/tag/v1.15) - 2023-08-04
 

setup.py

@@ -23,7 +23,7 @@
 
 from setuptools import find_packages, setup
 
-version = "1.16dev"
+version = "1.16"
 dl_version = "master" if "dev" in version else "v{}".format(version)
 
 print(