From f4400829cf972544216a370f514e65e73efb6826 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 28 Aug 2026 16:30:17 +0200 Subject: [PATCH 1/2] Fixed the multiqc config to include all lanes per read direction per sample --- CHANGELOG.md | 1 + assets/multiqc_config.yml | 11 +++++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 368e199e8..73e7e4b71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -93,6 +93,7 @@ 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. ### Parameters diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d76c55b48..1159fcad4 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -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" From 9ee95759e33642f3aa2d9d27c58cdc0e2386cc32 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Aug 2026 14:46:07 +0000 Subject: [PATCH 2/2] [automated] Fix code linting --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73e7e4b71..10b10a5cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -93,7 +93,7 @@ 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. +- `multiqc_config.yml` to include all lanes per read direction in the General Statistics section. ### Parameters