Ecosyste.ms: Issues

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GitHub / MultiQC/MultiQC issues and pull requests

#2905 - Samtools: Add insert size to general stats table

Pull Request - State: closed - Opened by pontushojer 5 months ago
Labels: module: enhancement

#2904 - Docs: embed generated-index into index.mdx

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: documentation

#2903 - Docs: build modules index page with a table

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 2 comments
Labels: documentation

#2902 - `cond_formatting_rules` fails in strict mode with numbers

Issue - State: closed - Opened by schorlton-bugseq 5 months ago - 1 comment
Labels: bug: core

#2901 - Fix generalstats headers key name in documentation

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: documentation, custom-content

#2900 - Regression: General Stats Custom Content Configuration No Longer Works in 1.25

Issue - State: closed - Opened by schorlton-bugseq 5 months ago - 2 comments
Labels: documentation, custom-content

#2899 - Small config validation improvements

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: back end

#2898 - Docs: overview page heading

Pull Request - State: closed - Opened by ewels 5 months ago
Labels: documentation

#2897 - samtools stats: add insert size to general statistics

Issue - State: closed - Opened by almahans 5 months ago - 1 comment
Labels: module: enhancement

#2896 - Update docs on admonitions

Pull Request - State: closed - Opened by ewels 5 months ago
Labels: documentation

#2895 - Kraken: fix minimizers heatmap

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: bug: module

#2894 - Remove the separate Bracken module as it just uses Kraken internally

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: change

#2893 - Bump 1.25.1

Pull Request - State: closed - Opened by vladsavelyev 5 months ago

#2892 - Support Python 3.8

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: infrastructure

#2891 - Strip out docs machinery, update a lot of links

Pull Request - State: closed - Opened by ewels 5 months ago
Labels: documentation

#2890 - Docs migrate v2

Pull Request - State: closed - Opened by ewels 5 months ago - 1 comment
Labels: documentation

#2889 - Suppress "SyntaxWarning: invalid escape sequence" warning from `colormath`

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: infrastructure

#2888 - Disable plot export in incompatible architecture containers (when running through rosetta)

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: back end

#2887 - Remove weird import and fix image build

Pull Request - State: closed - Opened by vladsavelyev 5 months ago

#2886 - Build docker image on any commit

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: infrastructure

#2885 - picard: Add table with all metrics to VariantCallingMetrics section

Pull Request - State: closed - Opened by spaul91 5 months ago - 5 comments
Labels: module: enhancement

#2884 - Docker image failes to build

Issue - State: closed - Opened by jchorl 5 months ago - 3 comments
Labels: core: infrastructure

#2883 - table_sample_merge to multiqc_config.yml cause the missing of modules

Issue - State: closed - Opened by LilyAnderssonLee 5 months ago - 1 comment
Labels: waiting: example data

#2882 - bbmap: support qhist with only R1 and extra header

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: bug: module

#2881 - Kraken: re-add the Unclassified tab to the Top taxa barplot

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: enhancement

#2880 - Picard HsMetrics: fix collecting data sources

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: bug: module

#2879 - Fix export general stats to `multiqc_data.json`: flatten row groups for back-compatibility

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: back end

#2878 - [not an issue] MultiQC v1.25 does not work with FastP output

Issue - State: closed - Opened by mdtorohernando 5 months ago - 4 comments

#2877 - Picard HsMetrics module not storing corrrect file paths into source list

Issue - State: closed - Opened by ccwang002 5 months ago - 1 comment
Labels: bug: module

#2876 - Kraken plot not displayed in MultiQC after version 1.23

Issue - State: closed - Opened by nschcolnicov 5 months ago - 6 comments
Labels: waiting: example data

#2875 - Custom tables: ignore unrecognized fields instead of failing

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment
Labels: bug: core, custom-content

#2874 - Update overview-svg-inline

Pull Request - State: closed - Opened by ewels 5 months ago

#2873 - Update overview-svg-inline

Pull Request - State: closed - Opened by ewels 5 months ago - 1 comment

#2872 - Bclconvert: group samples and lanes, refactor

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: enhancement

#2871 - Table sample groups: allow clicking the entire row to expand, add cursor pointer

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: front end

#2870 - v1.25: `ColumnMeta` object has no field `group`

Issue - State: closed - Opened by luisas 5 months ago - 1 comment
Labels: bug: core, custom-content

#2869 - pychopper module: add reads stats information

Issue - State: closed - Opened by rabioinf 5 months ago - 3 comments
Labels: waiting: response, module: enhancement

#2868 - ataqv

Issue - State: closed - Opened by pontushojer 5 months ago - 2 comments
Labels: module: new

#2867 - V1.25 in conda end up properly but not in the container distributed by biocontainers

Issue - State: closed - Opened by Juke34 5 months ago - 4 comments
Labels: kaleido

#2866 - BBMap report

Issue - State: closed - Opened by Juke34 5 months ago - 1 comment
Labels: bug: module

#2864 - bcl2fastq type hints

Pull Request - State: closed - Opened by vladsavelyev 5 months ago

#2863 - error

Issue - State: closed - Opened by sadboy123-sketch 5 months ago

#2862 - Support Python 3.13, drop 3.8

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment
Labels: core: refactoring

#2861 - CellRanger: Support for CellRanger Multi

Pull Request - State: open - Opened by Sxmple-DavidSchmidt 5 months ago - 4 comments
Labels: waiting: response, module: enhancement

#2860 - Group samples: Minor tweak suggestions

Issue - State: closed - Opened by ewels 5 months ago
Labels: core: front end

#2859 - Generate new screengrabs with rich-codex

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment

#2858 - Bump v1.25

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment

#2857 - Add remaining metrics to Picard submodule's `VariantCallingMetrics`

Issue - State: closed - Opened by spaul91 5 months ago - 1 comment
Labels: module: enhancement

#2856 - Fix FASTQC Per Base Sequence Content plot click when module run multiple times

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: bug: module

#2855 - Custom content in general stats table not working

Issue - State: closed - Opened by quiocarbajal 5 months ago - 1 comment
Labels: custom-content

#2854 - ngsbits: add submodule samplegender

Pull Request - State: closed - Opened by peterpru 5 months ago - 12 comments
Labels: module: enhancement

#2853 - Improve custom content documentation

Issue - State: open - Opened by vladsavelyev 5 months ago - 1 comment
Labels: documentation

#2852 - NanoStat: support multi-sample logs

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: enhancement

#2851 - Allow `x_band`, `x_lines`, `x_minrange` for any plot type (specifically scatter)

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: front end

#2850 - Mypy fixes for in plots

Pull Request - State: closed - Opened by vladsavelyev 5 months ago

#2849 - Custom content minor fixes

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment
Labels: custom-content

#2848 - Use classes for column/row hiding - fixes hiding in expanded groups

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: front end

#2847 - Support boxplot in custom content

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment
Labels: custom-content

#2846 - Add `py.typed` to mark package as providing type information

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: infrastructure

#2845 - Fix bar plot export from toolbox

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: front end

#2844 - Fix autoselection in plot export toolbox

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: front end

#2843 - Barplot Data TSV/CSV Export Missing Sample Names

Issue - State: closed - Opened by diderote 5 months ago - 1 comment
Labels: core: front end

#2842 - Add a py.typed file for downstream plugins to use MultiQC's type annotations

Issue - State: closed - Opened by ccwang002 5 months ago - 1 comment
Labels: core: infrastructure

#2841 - Fix replace_samples for custom content genstats table

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: custom-content

#2840 - Samtools coverage: suppot `exclude_contigs` and `include_contigs`

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 2 comments
Labels: module: enhancement

#2839 - Boxplots for custom content

Issue - State: closed - Opened by JohannesKersting 5 months ago - 2 comments
Labels: custom-content

#2838 - Ganon: support non-verbose output, fix missing `removed with --min-count`

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: enhancement

#2836 - Run plot export in threads with a time out and handle freezes

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: back end

#2835 - Custom data for many samples as barplot

Issue - State: closed - Opened by jd3234 5 months ago - 1 comment
Labels: asking-for-help

#2834 - fastp: support `--merged` flag

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: module: enhancement

#2833 - More type hinting

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: core: refactoring

#2832 - Standardise doc titles

Pull Request - State: closed - Opened by christopher-hakkaart 5 months ago

#2831 - Add sample-grouping docs

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 2 comments
Labels: documentation

#2830 - Fix hiding columns for grouped samples

Pull Request - State: closed - Opened by vladsavelyev 5 months ago

#2829 - Fix copy multiqc.log into multiqc_data output folder

Pull Request - State: closed - Opened by vladsavelyev 5 months ago
Labels: bug: core

#2828 - When both `contents` and `contents_re` are specified in a search patterns, treat it as logical AND

Pull Request - State: closed - Opened by vladsavelyev 5 months ago - 1 comment
Labels: core: back end

#2827 - Modify UMICollapse module to support FastQ mode.

Pull Request - State: closed - Opened by MatthiasZepper 5 months ago - 3 comments
Labels: module: enhancement

#2826 - Fastp module lacks on after trimming represention when fastp command runs with the `-m/--merge` option

Issue - State: closed - Opened by Daniel-VM 5 months ago - 4 comments
Labels: waiting: example data, module: enhancement

#2825 - Kraken2 report identified as Bracken

Issue - State: closed - Opened by marchoeppner 5 months ago - 1 comment
Labels: waiting: response

#2824 - TMB

Issue - State: open - Opened by bounlu 6 months ago
Labels: module: new

#2823 - Picard: fix parsing Sentieon IS metrics

Pull Request - State: closed - Opened by vladsavelyev 6 months ago
Labels: bug: module

#2819 - Wrap exporting flat plots in try-catch

Pull Request - State: closed - Opened by vladsavelyev 6 months ago
Labels: core: back end

#2814 - Add UMICollapse module

Pull Request - State: closed - Opened by siddharthab 6 months ago - 5 comments
Labels: module: new, waiting: example data

#2812 - nf-core pipeline crashes when using quay.io/biocontainers/multiqc > v1.21

Issue - State: closed - Opened by kedhammar 6 months ago - 2 comments
Labels: core: back end, kaleido

#2810 - FastQC: Incorrect mean average sequence length reported after trimming

Issue - State: closed - Opened by TBradley27 6 months ago - 2 comments
Labels: bug: module

#2809 - Pydantic errors with new AnchorT type

Issue - State: closed - Opened by Sxmple-DavidSchmidt 6 months ago - 6 comments

#2806 - Unable to generate `multiqc.log` file despite `--no-clean-up`

Issue - State: closed - Opened by jfy133 6 months ago - 1 comment
Labels: bug: core

#2805 - Ganon: support output w/o `--verbose`, fix for missing `removed with --min-count` line

Issue - State: closed - Opened by jfy133 6 months ago - 4 comments
Labels: bug: module

#2803 - Fix the WebAssembly runner https://multiqc.info/run runner

Issue - State: closed - Opened by vladsavelyev 6 months ago - 2 comments
Labels: priority: high, core: infrastructure

#2802 - samtools coverage: add include/exclude contigs option

Issue - State: closed - Opened by matthdsm 6 months ago - 2 comments
Labels: module: enhancement

#2801 - Kraken not being added to multiqc report after going from 1.23 to 1.24.1

Issue - State: closed - Opened by nschcolnicov 6 months ago - 3 comments
Labels: bug: module

#2798 - support for TELSEQ

Issue - State: closed - Opened by lindenb 6 months ago
Labels: module: new

#2795 - Config file seemingly not being respected

Issue - State: closed - Opened by stkgo 6 months ago - 1 comment
Labels: bug: core

#2794 - Group read pairs in general stats

Pull Request - State: closed - Opened by vladsavelyev 6 months ago - 5 comments
Labels: core: back end

#2791 - FastQC: fix positioning plot status labels when custom anchors set

Pull Request - State: closed - Opened by vladsavelyev 6 months ago - 1 comment
Labels: bug: module

#2790 - FastQC: use interval start instead of average for plots with bp as X axis

Pull Request - State: closed - Opened by vladsavelyev 6 months ago
Labels: module: enhancement

#2788 - Freyja: handle empty input, deterministic sample order

Pull Request - State: closed - Opened by vladsavelyev 6 months ago
Labels: bug: module, module: enhancement

#2787 - Heatmap: allow numeric `xcats` and `ycats`

Pull Request - State: closed - Opened by vladsavelyev 6 months ago - 1 comment
Labels: custom-content