From ea182023b51000b19c636fc5b2dea4b1282500ac Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 26 Nov 2024 15:16:32 +0100 Subject: [PATCH 1/2] add somalier reports to multiqc output --- workflows/germline.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/germline.nf b/workflows/germline.nf index d4d4a792..33d0c76e 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -608,6 +608,8 @@ workflow GERMLINE { ch_versions = ch_versions.mix(VCF_EXTRACT_RELATE_SOMALIER.out.versions) ch_final_peds = VCF_EXTRACT_RELATE_SOMALIER.out.peds ch_final_reports = ch_final_reports.mix(VCF_EXTRACT_RELATE_SOMALIER.out.html) + ch_reports = ch_reports.mix(VCF_EXTRACT_RELATE_SOMALIER.out.pairs_tsv.map { _meta, report -> report }) + ch_reports = ch_reports.mix(VCF_EXTRACT_RELATE_SOMALIER.out.samples_tsv.map { _meta, report -> report }) // // Add PED headers to the VCFs From 753069f01cb9a1afbca70e93047de11ea8adc480 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 26 Nov 2024 15:18:42 +0100 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d7732756..71670560 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 3. Completely reworked the output directory structure to a more sensible structure. The pipeline can now be run on the same output directory every time and will incrementally add files to the correct family folder. See the [output documentation](https://nf-cmgg.github.io/germline/latest/output/) for more info. 4. Migrated to the new workflow output definitions. 5. Bumped the minimal Nextflow version to 24.10.0. +6. Added the somalier reports to the multiQC report. ### Fixes