From dc200a551f2fd1771499a45d3162fc8d4143d65b Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Mon, 25 Nov 2024 15:04:37 +0100 Subject: [PATCH] MultiQC v1.25.2 (#313) * MultiQC v1.25.2 changelog * Update changelog/multiqc/v1.25.2.mdx Co-authored-by: Justine Geffen Signed-off-by: Phil Ewels --------- Signed-off-by: Phil Ewels Co-authored-by: Phil Ewels Co-authored-by: Justine Geffen --- 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..3d2ccd470 --- /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 */} + +### 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)) +- 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))