MultiQC/MultiQC issues and pull requests

#2873 - Update overview-svg-inline

Pull Request - State: closed - Opened by ewels 2 months ago - 1 comment

#2872 - Bclconvert: group samples and lanes, refactor

Pull Request - State: closed - Opened by vladsavelyev 2 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 2 months ago
Labels: core: front end

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

Issue - State: closed - Opened by luisas 2 months ago - 1 comment
Labels: bug: core, custom-content

#2869 - pychopper module: add reads stats information

Issue - State: open - Opened by rabioinf 2 months ago
Labels: module: enhancement

#2868 - ataqv

Issue - State: open - Opened by pontushojer 2 months ago - 1 comment
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 2 months ago - 4 comments
Labels: kaleido

#2866 - BBMap report

Issue - State: closed - Opened by Juke34 2 months ago - 1 comment
Labels: bug: module

#2865 - Check `add_data_source` args (either `path` or `f` should be specified), use `strict_helpers.lint_error`

Pull Request - State: closed - Opened by vladsavelyev 2 months ago
Labels: core: refactoring

#2864 - bcl2fastq type hints

Pull Request - State: closed - Opened by vladsavelyev 2 months ago

#2863 - error

Issue - State: closed - Opened by sadboy123-sketch 2 months ago

#2862 - Support Python 3.13, drop 3.8

Pull Request - State: closed - Opened by vladsavelyev 2 months ago - 1 comment
Labels: core: refactoring

#2861 - CellRanger: Support for CellRanger Multi

Pull Request - State: open - Opened by Sxmple-DavidSchmidt 2 months ago - 3 comments
Labels: waiting: response, module: enhancement

#2860 - Group samples: Minor tweak suggestions

Issue - State: open - Opened by ewels 2 months ago

#2859 - Generate new screengrabs with rich-codex

Pull Request - State: closed - Opened by vladsavelyev 2 months ago - 1 comment

#2858 - Bump v1.25

Pull Request - State: closed - Opened by vladsavelyev 2 months ago - 1 comment

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

Issue - State: closed - Opened by spaul91 2 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 2 months ago
Labels: bug: module

#2855 - Custom content in general stats table not working

Issue - State: closed - Opened by quiocarbajal 2 months ago - 1 comment
Labels: custom-content

#2854 - ngsbits: add submodule samplegender

Pull Request - State: closed - Opened by peterpru 2 months ago - 12 comments
Labels: module: enhancement

#2853 - Improve custom content documentation

Issue - State: open - Opened by vladsavelyev 2 months ago - 1 comment
Labels: documentation

#2852 - NanoStat: support multi-sample logs

Pull Request - State: closed - Opened by vladsavelyev 2 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 2 months ago
Labels: core: front end

#2850 - Mypy fixes for in plots

Pull Request - State: closed - Opened by vladsavelyev 2 months ago

#2849 - Custom content minor fixes

Pull Request - State: closed - Opened by vladsavelyev 2 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 2 months ago
Labels: core: front end

#2847 - Support boxplot in custom content

Pull Request - State: closed - Opened by vladsavelyev 2 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 2 months ago
Labels: core: infrastructure

#2845 - Fix bar plot export from toolbox

Pull Request - State: closed - Opened by vladsavelyev 2 months ago
Labels: core: front end

#2844 - Fix autoselection in plot export toolbox

Pull Request - State: closed - Opened by vladsavelyev 2 months ago
Labels: core: front end

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

Issue - State: closed - Opened by diderote 2 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 2 months ago - 1 comment
Labels: core: infrastructure

#2841 - Fix replace_samples for custom content genstats table

Pull Request - State: closed - Opened by vladsavelyev 2 months ago
Labels: custom-content

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

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

#2839 - Boxplots for custom content

Issue - State: closed - Opened by JohannesKersting 2 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 2 months ago
Labels: module: enhancement

#2837 - Remove `pyaml_env` dependency and apply the fix for the `SyntaxWarning`

Pull Request - State: closed - Opened by vladsavelyev 2 months ago

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

Pull Request - State: closed - Opened by vladsavelyev 2 months ago
Labels: core: back end

#2835 - Custom data for many samples as barplot

Issue - State: closed - Opened by jd3234 2 months ago - 1 comment
Labels: asking-for-help

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

Pull Request - State: closed - Opened by vladsavelyev 3 months ago
Labels: module: enhancement

#2833 - More type hinting

Pull Request - State: closed - Opened by vladsavelyev 3 months ago
Labels: core: refactoring

#2832 - Standardise doc titles

Pull Request - State: closed - Opened by christopher-hakkaart 3 months ago

#2831 - Add sample-grouping docs

Pull Request - State: closed - Opened by vladsavelyev 3 months ago - 2 comments
Labels: documentation

#2830 - Fix hiding columns for grouped samples

Pull Request - State: closed - Opened by vladsavelyev 3 months ago

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

Pull Request - State: closed - Opened by vladsavelyev 3 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 3 months ago - 1 comment
Labels: core: back end

#2827 - Modify UMICollapse module to support FastQ mode.

Pull Request - State: closed - Opened by MatthiasZepper 3 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 3 months ago - 4 comments
Labels: waiting: example data, module: enhancement

#2825 - Kraken2 report identified as Bracken

Issue - State: closed - Opened by marchoeppner 3 months ago - 1 comment
Labels: waiting: response

#2824 - TMB

Issue - State: open - Opened by bounlu 3 months ago
Labels: module: new

#2823 - Picard: fix parsing Sentieon IS metrics

Pull Request - State: closed - Opened by vladsavelyev 3 months ago
Labels: bug: module

#2819 - Wrap exporting flat plots in try-catch

Pull Request - State: closed - Opened by vladsavelyev 3 months ago
Labels: core: back end

#2814 - Add UMICollapse module

Pull Request - State: closed - Opened by siddharthab 3 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 3 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 3 months ago - 2 comments
Labels: bug: module

#2809 - Pydantic errors with new AnchorT type

Issue - State: closed - Opened by Sxmple-DavidSchmidt 3 months ago - 6 comments

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

Issue - State: closed - Opened by jfy133 3 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 3 months ago - 4 comments
Labels: bug: module

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

Issue - State: closed - Opened by vladsavelyev 3 months ago - 2 comments
Labels: priority: high, core: infrastructure

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

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

#2795 - Config file seemingly not being respected

Issue - State: closed - Opened by stkgo 3 months ago - 1 comment
Labels: bug: core

#2794 - Group read pairs in general stats

Pull Request - State: closed - Opened by vladsavelyev 3 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 3 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 3 months ago
Labels: module: enhancement

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

Pull Request - State: closed - Opened by vladsavelyev 3 months ago
Labels: bug: module, module: enhancement

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

Pull Request - State: closed - Opened by vladsavelyev 3 months ago - 1 comment
Labels: custom-content

#2786 - Fix for Python 3.8

Pull Request - State: closed - Opened by vladsavelyev 3 months ago

#2783 - Fix configuring `extra_fn_clean_exts` and `fn_clean_exts` conflict with each other

Pull Request - State: closed - Opened by jchorl 3 months ago - 1 comment
Labels: bug: core

#2766 - Issue with Sample Names and Custom Content

Issue - State: closed - Opened by whottel 3 months ago - 4 comments
Labels: custom-content

#2764 - samtools stats incorrect reporting when omitting duplicates

Issue - State: closed - Opened by pdimens 3 months ago - 11 comments
Labels: waiting: example data

#2746 - [module] GATK/DepthOfCoverage

Issue - State: open - Opened by adamrtalbot 4 months ago
Labels: module: new

#2742 - sentieon/qualcal

Issue - State: open - Opened by adamrtalbot 4 months ago - 4 comments
Labels: module: new

#2729 - Improved docs on multiqc.get_plot for sections with subsections

Issue - State: closed - Opened by nick-youngblut 4 months ago - 1 comment

#2699 - Adding mgikit plugin

Pull Request - State: open - Opened by ziadbkh 4 months ago
Labels: module: new, WIP

#2699 - Adding mgikit plugin

Pull Request - State: open - Opened by ziadbkh 4 months ago
Labels: module: new, WIP

#2667 - 1.22.3 Hanging in MacOS Docker, in nf-core/rnaseq

Issue - State: closed - Opened by pinin4fjords 5 months ago - 19 comments
Labels: core: back end, kaleido

#2643 - Docs refactoring

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

#2640 - Updating NanoStat/NanoPlot Quality Score thresholds from Q5-Q15 to Q10-Q30

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

#2609 - Fix `re_contents` search patterns when pattern is in the middle of the file

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

#2608 - incorporating CollectRnaSeqMetrics output in report

Issue - State: open - Opened by MSaadfarooq 6 months ago - 5 comments
Labels: waiting: example data

#2533 - Interactive usage: additive `multiqc.parse_logs()` sample parsing

Issue - State: open - Opened by vladsavelyev 7 months ago
Labels: core: back end

#2518 - Faster JSON dumping.

Issue - State: open - Opened by rhpvorderman 7 months ago - 1 comment
Labels: core: back end

#2507 - Add ngs-bits SampleGender output to MultiQC

Issue - State: closed - Opened by peterpru 7 months ago - 2 comments
Labels: module: new

#2467 - Custom data grouping into different subtabs

Issue - State: open - Opened by jdcla 8 months ago
Labels: custom-content

#2466 - Add screenshot examples for line plot categories

Pull Request - State: closed - Opened by vladsavelyev 8 months ago - 1 comment

#2463 - Make remove_sections option fully exclude plot data

Pull Request - State: closed - Opened by vladsavelyev 8 months ago - 1 comment

#2417 - Stylize "Percentages" and "Log10" buttons as toggles

Issue - State: open - Opened by tamuanand 9 months ago - 6 comments
Labels: core: front end

#2398 - Bump versions for v1.21 release [skip changelog]

Pull Request - State: closed - Opened by vladsavelyev 9 months ago - 1 comment

#2367 - Add a "box plot" view to the line plot

Issue - State: open - Opened by vladsavelyev 9 months ago
Labels: core: front end

#2206 - Use `self.anchor` to prepend plot IDs to make sure custom anchor is applied

Pull Request - State: open - Opened by vladsavelyev 12 months ago - 2 comments
Labels: core: back end, WIP

#2103 - Request module for cellranger multi

Issue - State: open - Opened by pcm32 about 1 year ago - 3 comments
Labels: module: new

#2076 - Dynamically use `self.anchor` for plots' and sections' IDs

Issue - State: open - Opened by sstrong99 about 1 year ago - 4 comments
Labels: core: back end, breaking change

#1953 - Scatter plot "xPlotBands" and "yPlotBands" do not render in the correct order if custom "data_labels" are provided

Issue - State: closed - Opened by buijt over 1 year ago - 1 comment
Labels: bug: core, core: front end, priority: low

GitHub / MultiQC/MultiQC issues and pull requests