MultiQC/MultiQC issues and pull requests

#3090 - conda install of version 1.27.1 doesn't work

Issue - State: open - Opened by agroppi 4 days ago - 1 comment

#3089 - The 'trimmomatic' MultiQC module broke when executing multiqc

Issue - State: open - Opened by zyjbird 5 days ago

#3088 - String/Number format errors during report generation using custom config.yml

Issue - State: open - Opened by pkerbs 8 days ago

#3087 - Bump 1.27.1

Pull Request - State: closed - Opened by vladsavelyev 11 days ago - 1 comment

#3086 - Handle empty custom content files

Pull Request - State: closed - Opened by vladsavelyev 11 days ago
Labels: custom-content

#3085 - MultiQC 1.27 crashes on empty custom content file

Issue - State: closed - Opened by Redmar-van-den-Berg 12 days ago - 1 comment
Labels: custom-content

#3084 - Change Sequali DOI to article link

Pull Request - State: closed - Opened by rhpvorderman 13 days ago

#3083 - Add option to provider custom OpenAI endpoint

Pull Request - State: closed - Opened by vladsavelyev 13 days ago
Labels: ai

#3082 - Table scatters: support hide, rename, highlight

Pull Request - State: closed - Opened by vladsavelyev 13 days ago
Labels: core: front end

#3081 - Table scatter plot: remove legend to make more space

Pull Request - State: closed - Opened by vladsavelyev 13 days ago
Labels: core: front end

#3080 - No analysis results found. Cleaning up..

Issue - State: closed - Opened by jingjojojo 14 days ago - 1 comment

#3079 - Custom content: using `section_comments` along with `parent_id`

Issue - State: closed - Opened by Hanjiewu 15 days ago - 1 comment
Labels: custom-content

#3078 - Always save prompt to file

Pull Request - State: closed - Opened by vladsavelyev 18 days ago
Labels: ai

#3077 - Box plot AI repro: use statistics instead of raw values, support static version

Pull Request - State: closed - Opened by vladsavelyev 18 days ago
Labels: ai

#3076 - AI: Config option to customise endpoint

Issue - State: closed - Opened by achakkas 19 days ago - 4 comments
Labels: planned, ai

#3075 - FastQC: fix "Per Base Sequence Content" heatmap

Pull Request - State: closed - Opened by vladsavelyev 19 days ago
Labels: bug: core

#3074 - Anonymize sample names

Pull Request - State: closed - Opened by vladsavelyev 19 days ago
Labels: planned, ai

#3073 - Possible Typo in bclconvert module - Sample Stats Column header for "Mean quality score"

Issue - State: closed - Opened by tamuanand 20 days ago - 1 comment

#3072 - Config from env: resolve empty to Null

Pull Request - State: closed - Opened by vladsavelyev 20 days ago
Labels: core: back end

#3071 - Make token count warning a debug

Pull Request - State: closed - Opened by vladsavelyev 20 days ago
Labels: ai

#3070 - Token count warning log should be debug

Issue - State: closed - Opened by ewels 21 days ago
Labels: ai

#3069 - Refactor plotting code to save and load input data

Pull Request - State: open - Opened by vladsavelyev 21 days ago

#3068 - When "Clear summary" clicked on global, clear also the generated extended summary

Pull Request - State: closed - Opened by vladsavelyev 21 days ago
Labels: ai

#3067 - Add "Chat with Seqera AI" buttons to all summaries

Pull Request - State: closed - Opened by vladsavelyev 21 days ago
Labels: ai

#3066 - Remove `langchain` dependency

Pull Request - State: closed - Opened by vladsavelyev 22 days ago
Labels: ai

#3065 - OpenAI model names

Issue - State: closed - Opened by agroppi 22 days ago - 6 comments
Labels: ai

#3064 - Use `tiktoken` to estimate token counts for all providers

Pull Request - State: closed - Opened by vladsavelyev 22 days ago
Labels: ai

#3063 - Do not print stack trace on KeyboardInterrupt unless verbose

Pull Request - State: closed - Opened by vladsavelyev 22 days ago
Labels: core: back end

#3062 - Add "Chat with Seqera AI" to plots and tables summaries

Issue - State: closed - Opened by vladsavelyev 22 days ago
Labels: ai

#3061 - Please allow hiding sample names from scatter plots

Issue - State: closed - Opened by charles-plessy 22 days ago - 2 comments
Labels: core: front end, planned

#3060 - Anonymise sample IDs for AI summaries

Issue - State: closed - Opened by ewels 25 days ago - 2 comments
Labels: planned, ai

#3059 - Parsing custom content TSV: allow leading empty columns

Pull Request - State: closed - Opened by vladsavelyev 26 days ago
Labels: custom-content

#3058 - Custom content: Support `.gif`, `.webp` and `.tiff`

Pull Request - State: closed - Opened by ewels 26 days ago
Labels: custom-content

#3057 - Generate new screengrabs with rich-codex

Pull Request - State: closed - Opened by vladsavelyev 26 days ago

#3056 - Update module docs

Pull Request - State: closed - Opened by vladsavelyev 26 days ago
Labels: documentation

#3055 - AI: handle interrupted streaming with an error notice

Pull Request - State: open - Opened by vladsavelyev 27 days ago
Labels: core: front end, ai

#3054 - Lowercase AI buttons

Pull Request - State: closed - Opened by vladsavelyev 27 days ago

#3053 - Support bustools 0.44.1

Pull Request - State: closed - Opened by vladsavelyev 27 days ago
Labels: module: enhancement

#3052 - Bump v1.27

Pull Request - State: closed - Opened by vladsavelyev 27 days ago

#3051 - Request module for squab counter

Issue - State: open - Opened by abearab 29 days ago - 3 comments
Labels: module: new, waiting: example data

#3050 - AI: Wrap Seqera AI prompt in `<details>`

Pull Request - State: closed - Opened by ewels about 1 month ago - 4 comments

#3049 - `bustools` module not compatible with latest release (0.44.1)

Issue - State: closed - Opened by jdidion about 1 month ago - 1 comment
Labels: module: enhancement

#3048 - Update ruff and pre-commit

Pull Request - State: closed - Opened by vladsavelyev about 1 month ago
Labels: core: infrastructure

#3047 - Reproduce runs from `multiqc_data.json`

Pull Request - State: open - Opened by vladsavelyev about 1 month ago
Labels: core: back end, planned

#3046 - Checkm2: handle v1.0.1, be less strict to header columns

Pull Request - State: closed - Opened by vladsavelyev about 1 month ago
Labels: module: enhancement

#3045 - Make tables Configure Column max columns configurable

Pull Request - State: closed - Opened by vladsavelyev about 1 month ago
Labels: bug: core, core: front end

#3044 - Preserve order of `saved_raw_data_keys`

Pull Request - State: closed - Opened by vladsavelyev about 1 month ago
Labels: core: back end

#3043 - Mixed sorting in report_saved_raw_data part of report

Issue - State: closed - Opened by Stikus about 1 month ago - 2 comments

#3042 - Visualization of wide tables

Issue - State: closed - Opened by Stikus about 1 month ago - 1 comment
Labels: bug: core, core: front end

#3041 - Add "Continue with Seqera AI" button

Pull Request - State: closed - Opened by vladsavelyev about 1 month ago - 1 comment
Labels: awaits-review

#3040 - CheckM2 output format different in v1.0.1

Issue - State: closed - Opened by patriciatran about 1 month ago - 2 comments
Labels: bug: module

#3039 - fastp module: validation warning

Issue - State: closed - Opened by guidohooiveld about 1 month ago - 1 comment

#3038 - Preseq: fix parsing `nan` and add strict type hints

Pull Request - State: closed - Opened by vladsavelyev about 2 months ago
Labels: bug: module

#3037 - Preseq TypeError

Issue - State: closed - Opened by guidohooiveld about 2 months ago - 5 comments
Labels: bug: module

#3036 - Soliciting tool for MultiQC

Issue - State: closed - Opened by BiomedicLJZ about 2 months ago - 1 comment
Labels: module: new

#3035 - Heatmap: add clustering view

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

#3034 - Improve config validation: print path in config, shorten lists in error messages

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

#3033 - Align order of lineplot categories across samples

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

#3032 - Mosdepth module: Axis order on "Average coverage per contig" plot

Issue - State: closed - Opened by tstoeriko 2 months ago - 1 comment
Labels: bug: core

#3031 - Update module docs to use along with `.cursorrules`

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

#3030 - Add pytest ini options to `pyproject.toml`

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

#3029 - Update ruff to v0.8.3

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

#3028 - Custom content tests: add more, and use files in test-data instead of hardcoded snippets

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

#3027 - Tweak organisaion of CLI flags in help

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

#3026 - Bump v1.26

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

#3025 - Add Cursor rules for module generation

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

#3024 - Pychopper: add UMI barpot

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

#3023 - New module: mgikit

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

#3022 - Sample grouping: add docs example how to group by lane and read type

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

#3021 - phantompeakqualtools: Adjust minimum value to 1 for NSC coeff

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

#3020 - Custom content: allow quoting values in CSV

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

#3019 - Override data types of table columns for custom content

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

#3018 - QualiMap RNASeq: add gen stats columns for exonic, intronic, intergenic, overlapping

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

#3017 - RNA SeqC: more metrics in gen stats

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

#3016 - Add RNA-SeQC metrics to general statistics

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

#3015 - Add qualimap rnaseq metrics to general statistics

Issue - State: closed - Opened by mtochilkina 2 months ago - 1 comment

#3014 - Question: how to visualize several FastQC reports for one sample

Issue - State: closed - Opened by serge2016 2 months ago - 2 comments
Labels: asking-for-help

#3013 - Add module ataqv

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

#3012 - DRAGEN: RNA quant metrics: support forward and reverse fragments in barplot

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

#3011 - New module: percolator: a semi-supervised learning framework for peptide identification from shotgun proteomics datasets.

Pull Request - State: closed - Opened by JuliaGraf 2 months ago - 10 comments
Labels: module: new

GitHub / MultiQC/MultiQC issues and pull requests