From 09310396c27563adc15e5cdb86f5f35500b93bbe Mon Sep 17 00:00:00 2001 From: vladsaveliev Date: Wed, 20 Nov 2024 20:45:09 +0100 Subject: [PATCH 1/2] MultiQC v1.25.2 changelog --- changelog/multiqc/v1.25.2.mdx | 55 +++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 changelog/multiqc/v1.25.2.mdx diff --git a/changelog/multiqc/v1.25.2.mdx b/changelog/multiqc/v1.25.2.mdx new file mode 100644 index 000000000..99483a42c --- /dev/null +++ b/changelog/multiqc/v1.25.2.mdx @@ -0,0 +1,55 @@ +--- +title: MultiQC v1.25.2 +date: 2024-11-20 +tags: [multiqc] +--- + +Multiple bug fixes and minor updates. + +{/* truncate */} + +### Updates + +- Add natural sort for sample sorting ([#2959](https://github.com/MultiQC/MultiQC/pull/2959)) +- Custom content: for `plot_type: image`, support `custom_data` config with section name and description. Fix misleading logging ([#2939](https://github.com/MultiQC/MultiQC/pull/2939)) +- Config validation improvements (group messages, cast types, validate column headers) ([#2899](https://github.com/MultiQC/MultiQC/pull/2899)) + +### Fixes + +- Workaround for displaying sample grouping in Safari because of missing `visibility: collapse` ([#2941](https://github.com/MultiQC/MultiQC/pull/2941)) +- Fix table CSV export where a title contains a comma ([#2911](https://github.com/MultiQC/MultiQC/pull/2911)) +- Showing table in notebooks: respect `col1_header` ([#2914](https://github.com/MultiQC/MultiQC/pull/2914)) +- Customizing `custom_table_header_config`: fix docs, support both the old and the new ways ([#2955](https://github.com/MultiQC/MultiQC/pull/2955)) +- Table scatter mini-plots: fix rounding and range ([#2956](https://github.com/MultiQC/MultiQC/pull/2956)) +- File line block iterator: fix reading long lines that do not fit one block ([#2935](https://github.com/MultiQC/MultiQC/pull/2935)) +- Fix `cond_formatting_rules` type hint to avoid validation error ([#2922](https://github.com/MultiQC/MultiQC/pull/2922)) +- Fix `config.prepend_dirs` or `-d -dd 1` ([#2913](https://github.com/MultiQC/MultiQC/pull/2913)) +- Sample grouping fixes ([#2920](https://github.com/MultiQC/MultiQC/pull/2920)): + - Keep sample name column fix width to avoid jumping + - Fix hiding columns through the modal +- Custom content fixes: + - Avoid showing `section_comment` both for module and section when they have the same ID ([#2954](https://github.com/MultiQC/MultiQC/pull/2954)) + - Address issue of sections without search patterns and headers in files ([#2921](https://github.com/MultiQC/MultiQC/pull/2921)) + - Fix duplicated custom content sections in the report ([#2921](https://github.com/MultiQC/MultiQC/pull/2921)) + - Fix support for `plot_type: violin` ([#2957](https://github.com/MultiQC/MultiQC/pull/2957)) + +### Module updates + +- ngsbits: add submodule samplegender ([#2854](https://github.com/MultiQC/MultiQC/pull/2854)) +- nanoq: change lineplots for barplots ([#2934](https://github.com/MultiQC/MultiQC/pull/2934)) +- Qualimap: clarify the direction of the transcript in coverage plot ([#2946](https://github.com/MultiQC/MultiQC/pull/2946)) +- picard: add table with all metrics to VariantCallingMetrics section ([#2885](https://github.com/MultiQC/MultiQC/pull/2885)) +- Nanostat: add general stats columns ([#2961](https://github.com/MultiQC/MultiQC/pull/2961)) +- Samtools: add insert size to general stats table ([#2905](https://github.com/MultiQC/MultiQC/pull/2905)) + +### Module fixes + +- bcl2fastq: fix missing `R1_*`/`R2_*` metrics ([#2965](https://github.com/MultiQC/MultiQC/pull/2965)) +- Cutadapt: fix for null values from r2 data ([#2936](https://github.com/MultiQC/MultiQC/pull/2936)) +- Qualimap: fix parsing ∞ value ([#2937](https://github.com/MultiQC/MultiQC/pull/2937)) +- bclconvert: fix undetermined barcodes plot ([#2976](https://github.com/MultiQC/MultiQC/pull/2976)) +- featurecounts: fix missing section name and anchor ([#2967](https://github.com/MultiQC/MultiQC/pull/2967)) + +### Infrastructure + +- Pin kaleido to 0.2.1 (new 0.4.1 does not embed a browser and thus not portable) ([#2963](https://github.com/MultiQC/MultiQC/pull/2963)) From e21456615ca208a8b82f6ca2cbc9a8123129b110 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 23 Nov 2024 14:51:14 +0100 Subject: [PATCH 2/2] Update changelog/multiqc/v1.25.2.mdx Co-authored-by: Justine Geffen Signed-off-by: Phil Ewels --- changelog/multiqc/v1.25.2.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/changelog/multiqc/v1.25.2.mdx b/changelog/multiqc/v1.25.2.mdx index 99483a42c..3d2ccd470 100644 --- a/changelog/multiqc/v1.25.2.mdx +++ b/changelog/multiqc/v1.25.2.mdx @@ -8,7 +8,7 @@ Multiple bug fixes and minor updates. {/* truncate */} -### Updates +### Feature updates and improvements - Add natural sort for sample sorting ([#2959](https://github.com/MultiQC/MultiQC/pull/2959)) - Custom content: for `plot_type: image`, support `custom_data` config with section name and description. Fix misleading logging ([#2939](https://github.com/MultiQC/MultiQC/pull/2939))