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MultiQC v1.29

MultiQC

Highlights​

BETA: MultiQC now writes out an Apache Parquet file multiqc_data/BETA-multiqc.parquet for each run containing plot and table data and metadata. This output is useful to:

  • Reproduce MultiQC runs without access to the original data.
  • Combine multiple MultiQC runs across different sampels or modules.
  • Populate an analytics database for e.g. time series analysis.

See the full documentation on using parquet output here.

Note that the format is unstable may change in the following release as we are still exploring the best format for the OLAP integration.

Feature updates and improvements​

  • Write plot and table data in a Parquet file (#3118, #3194, #3171, #3175)
  • Support Markdown in custom content (#3204)
  • AI summaries:
    • AWS Bedrock support for AI summaries (#3115) (#3115)
    • Allow customizing prompt sent to LLM (#3131)
    • Ignore formatting errors when generating AI summary from violin plot (#3129)
    • Headers for AzureAI: add config.ai_auth_type (#3122)
  • New CLI command: multiqc --check-config (#3120, #3147)
  • Allow both table ID and table anchor in table custom config (#3190)
  • Add option --only-samples - opposite of --ignore-samples (#3174)
  • Generalize customizing general stats columns (#3164)
  • Use killable processes for kaleido plot export (#3157)
  • Add timeout to plot export (#3111)
  • Customize plot subtitle ("N samples") (#3160)
  • Sort custom-content by section name by default (#3137)

New modules​

  • New module: Elembio bases2fastq (#3123)
  • New module: Elembio cells2stats (#3176)

Fixes​

  • Avoid crash if failed to remove the tmp dir (#3159)
  • Make sure multiqc.log has full debug log (#3173)
  • MegaQC config attribute fix (#3172)
  • Custom content: fix when section id and plot anchor are identical (#3184)
  • Fix false auto-opening toolbox when SeqeraAI is selected (#3193)
  • Fix applying data_labels extra parameters in plot config (#3181)
  • Handle timezone locale error (#3149)
  • Document multiqc.parse_logs("multiqc.parquet") (#3169)
  • Fix barplot CSV in-browser export (#3148)
  • Fix setting custom_table_header_config for custom table (#3135)
  • Coerce x-values to float when setting x-range on linegraph (#3130)
  • Fix pre-configured table sort defaultsort (#3140)
  • Fix barplot CSV in-browser export (#3148)
  • AI summaries:
    • Fix bug generating AI table from violin plot (#3128)

Module updates and fixes​

  • NanoStat: allow customizing general stats columns (#3163)
  • bcftools stats: enable log switch for indel plot (#3196)
  • Bases2Fastq: support handling of single end sequencing data (#3179)
  • Bases2Fastq: support handling of single-end sequencing data (#3189)
  • samtools: generalize customizing general stats columns (#3164)
  • samtools markdup: handle input with absolute paths (#3150)
  • NanoStat: allow customizing general stats columns (#3163)
  • Bases2Fastq: update links and definitions (#3158)
  • PRINSEQ++: fix logger warnings (#3198)
  • fastp: don't display decimal points on filtering result bar chart (#3132)
  • kraken: hide read-count decimals for taxa plot (#3143)