Merge pull request #240 from nf-cmgg/multiqc-test-somalier

Multiqc test somalier
nf-cmgg · Nov 26, 2024 · 20e256a · 20e256a
2 parents 6f24618 + 753069f
commit 20e256a
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diff --git 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
 

diff --git 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