nf-core · ramprasadn · Apr 22, 2025 · Apr 24, 2025 · Apr 29, 2025 · Apr 29, 2025
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/raredisease' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/raredisease' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/[email protected]
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
@@ -51,12 +30,12 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/raredisease/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/raredisease/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/raredisease/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/raredisease/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -67,5 +67,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -8,7 +8,7 @@ lint:
     - docs/images/nf-core-raredisease_logo_light.png
     - assets/nf-core-raredisease_logo_light.png
   modules_config: false
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: Clinical Genomics Stockholm
@@ -18,4 +18,4 @@ template:
   name: raredisease
   org: nf-core
   outdir: .
-  version: 2.5.0dev
+  version: 2.6.0dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.5.0dev - Cacofonix [XXXX-XX-XX]
+## 2.6.0dev - Cacofonix [XXXX-XX-XX]
 
 ### `Added`
 
@@ -52,6 +52,38 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | add_most_severe_consequence | 1.0         | 1.1         |
 | add_most_severe_pli         | 1.0         | 1.1         |
 
+## v2.5.0 - Fulliautomatix [2025-05-22]
+
+### `Added`
+
+- A new parameter `concatenate_snv_calls` to generate a concatenated VCF file containing unannotated nuclear & mitochondrial SNV calls [#699](https://github.com/nf-core/raredisease/pull/699)
+- Functionality to check contamination in samples using VerifyBamID2 [#701](https://github.com/nf-core/raredisease/pull/701)
+- New parameters `verifybamid_svd_bed`, `verifybamid_svd_mu`, and `verifybamid_svd_ud` to supply reference files for VerifyBamID2 [#701](https://github.com/nf-core/raredisease/pull/701)
+
+### `Changed`
+
+- Default to remove mitochondrial variants with FILTER status not equal to PASS [#697](https://github.com/nf-core/raredisease/pull/697)
+
+### `Fixed`
+
+- Sort the input files before vcf2cytosure is invoked [#697](https://github.com/nf-core/raredisease/pull/697)
+- Use '--mitochondria-mode' by default when running Gatk4 FilterMutectCalls on mitochondrial variants[#697](https://github.com/nf-core/raredisease/pull/697)
+
+### Parameters
+
+| Old parameter | New parameter         |
+| ------------- | --------------------- |
+|               | concatenate_snv_calls |
+|               | verifybamid_svd_bed   |
+|               | verifybamid_svd_mu    |
+|               | verifybamid_svd_ud    |
+
+### Tool updates
+
+| Tool         | Old version | New version |
+| ------------ | ----------- | ----------- |
+| VerifyBamID2 |             | 2.0.1       |
+
 ## 2.4.0 - Vitalstatistix [2025-02-24]
 
 ### `Added`

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -160,6 +160,10 @@
 
   > Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016;17(1):118. doi:10.1186/s13059-016-0973-5
 
+- [VerifyBamID2]()
+
+  > Zhang F, Flickinger M, Taliun SAG, Consortium IPG, Abecasis GR, Scott LJ, McCaroll SA, Pato CN, Boehnke M, & Kang HM. (2020). Ancestry-agnostic estimation of DNA sample contamination from sequence reads. Genome Research, 30(2), 185–194. https://doi.org/10.1101/gr.246934.118
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

diff --git a/README.md b/README.md
@@ -56,6 +56,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [Qualimap](http://qualimap.conesalab.org/)
 - [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)
 - [TIDDIT's cov](https://github.com/J35P312/)
+- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)
 
 **2. Alignment:**
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,13 +1,10 @@
 custom_logo: "nf-core-raredisease_logo_light.png"
 custom_logo_url: https://github.com/nf-core/raredisease/
 custom_logo_title: "nf-core/raredisease"
-
-report_comment: >2
-
-  This report has been generated by the <a href="https://github.com/nf-core/raredisease/tree/dev"
-  target="_blank">nf-core/raredisease</a> analysis pipeline. For information about
-  how to interpret these results, please see the <a href="https://nf-co.re/raredisease/dev/docs/output"
-  target="_blank">documentation</a>.
+report_comment: >
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.5.0" target="_blank">nf-core/raredisease</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/raredisease/2.5.0/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-raredisease-methods-description":
@@ -28,6 +25,7 @@ run_modules:
   - mosdepth
   - ngsbits
   - peddy
+  - verifybamid
   - custom_content
 
 module_order:
@@ -49,6 +47,8 @@ module_order:
       name: "ngsbits"
   - peddy:
       name: "Peddy"
+  - verifybamid:
+      name: "VerifyBamID2"
 
 extra_fn_clean_exts:
   - "_sorted_md"

diff --git a/conf/modules/align.config b/conf/modules/align.config
@@ -28,7 +28,7 @@ process{
 
     withName: '.*ALIGN:SAMTOOLS_VIEW' {
         ext.args   = { '--output-fmt cram --write-index' }
-        ext.prefix = { "${meta.id}_sorted_md" }
+        ext.prefix = { "${meta.id}_sort_md" }
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,

diff --git a/conf/modules/call_snv.config b/conf/modules/call_snv.config
@@ -22,4 +22,15 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: '.*CALL_SNV:BCFTOOLS_CONCAT' {
+        ext.args   = { "--write-index=tbi" }
+        ext.prefix = { "${meta.id}_mt_and_nuclear_snvs" }
+        publishDir = [
+            enabled: params.concatenate_snv_calls,
+            path: { "${params.outdir}/call_snv/concatenated_calls" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }
diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config
@@ -22,6 +22,7 @@ process {
     }
 
     withName: '.*CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT' {
+        ext.args   = '--mitochondria-mode'
         ext.prefix = { "${meta.id}_filtered" }
     }
 
@@ -46,6 +47,7 @@ process {
     }
 
     withName: '.*CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT' {
+        ext.args = '--mitochondria-mode'
         ext.prefix = { "${meta.id}_filtered_shifted" }
     }
 

diff --git a/conf/modules/postprocess_MT_calls.config b/conf/modules/postprocess_MT_calls.config
@@ -45,7 +45,7 @@ process {
     }
 
     withName: '.*POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE' {
-        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
+        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z --include FILTER='\"PASS\"'"
         ext.prefix = { "${meta.id}_mitochondria" }
         publishDir = [
             path: { "${params.outdir}/call_snv/mitochondria" },

diff --git a/docs/images/raredisease_metromap_dark.pdf b/docs/images/raredisease_metromap_dark.pdf
diff --git a/docs/images/raredisease_metromap_dark.png b/docs/images/raredisease_metromap_dark.png
diff --git a/docs/images/raredisease_metromap_dark.svg b/docs/images/raredisease_metromap_dark.svg
diff --git a/docs/images/raredisease_metromap_light.pdf b/docs/images/raredisease_metromap_light.pdf
diff --git a/docs/images/raredisease_metromap_light.png b/docs/images/raredisease_metromap_light.png