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MultiQC config fix to include all lanes per read direction in the general stats #1008

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MultiQC config fix to include all lanes per read direction in the general stats #1008

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f440082
Fixed the multiqc config to include all lanes per read direction per …
emmadizdarevic Aug 28, 2026
9ee9575
[automated] Fix code linting
nf-core-bot Aug 28, 2026
32e96c1
Merge branch 'dev' into fix-multiqc-read-stats
jemten Aug 28, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -123,6 +123,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix inconsistent sample column order in Sentieon SNV family VCF by sorting per-sample VCFs by filename before merging, consistent with DeepVariant and MT paths [#908](https://github.com/nf-core/raredisease/pull/908)
- Fix intermittent `CALL_SNV_DEEPVARIANT - wgs` test failure caused by non-deterministic GLnexus quality scores by replacing `variantsMD5` with `vcf.summary` [#850](https://github.com/nf-core/raredisease/pull/850)
- Fix swapped `run_mt_for_wes`/`skip_split_multiallelics` arguments in the `CALL_SNV` call, which disabled multiallelic splitting (and inverted MT-for-WES) when `--run_mt_for_wes` was set [#854](https://github.com/nf-core/raredisease/issues/854)
- `multiqc_config.yml` to include all lanes per read direction in the General Statistics section.

@jemten jemten Aug 28, 2026

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Suggested change
- `multiqc_config.yml` to include all lanes per read direction in the General Statistics section.
- Fix `multiqc_config.yml` to include all lanes per read direction in the General Statistics section. [#1008](https://github.com/nf-core/raredisease/pull/1008)


### Parameters

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11 changes: 9 additions & 2 deletions assets/multiqc_config.yml
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Expand Up @@ -83,14 +83,21 @@ table_columns_placement:
gatk_contamination:
contamination_pct: 900

fn_clean_sample_names: true

fn_clean_exts:
- ".gz"
- ".fastq"
- ".tsv"
- ".txt"
- ".bam"

extra_fn_clean_exts:
- "_sorted_md"
- "_contamination"
- "_pileups"
- "_mosdepth"
- "_sorted"
- type: regex
pattern: "_LNUMBER[0-9]{1,}"

table_sample_merge:
"(R1)": "_1"
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