Ncbench

.github/workflows/awstest.yml

@@ -15,8 +15,12 @@ on:
         description: "Trigger somatic full test on AWS"
         type: boolean
         default: false
-      germline:
-        description: "Trigger germline full test on AWS"
+      germline_wgs:
+        description: "Trigger germline full test (WGS) on AWS"
+        type: boolean
+        default: false
+      germline_wes:
+        description: "Trigger germline full test (WES) on AWS"
         type: boolean
         default: false
 
@@ -32,8 +36,11 @@ jobs:
             enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.profiletest ) }}
           - profile: test_full
             enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.somatic ) }}
-          - profile: test_full_germline
-            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline ) }}
+          - profile: test_full_germline_wgs
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wgs ) }}
+          - profile: test_full_germline_wes
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wes ) }}
+
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower

.github/workflows/ncbench.yml

@@ -0,0 +1,43 @@
+name: NCBench Zenodo Upload
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  # upload can only be triggered manually for now
+  workflow_dispatch:
+      inputs:
+        germline_wes:
+          description: "Trigger NCBench upload"
+          type: boolean
+          default: true
+
+jobs:
+  ncbench-upload:
+    name: Move files to Zenodo
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - profile: germline_wes
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wes ) }}
+    steps:
+      - name: Download files from AWS
+        uses: keithweaver/[email protected]
+        if: ${{ matrix.enabled }}
+        with:
+          revision: ${{ github.sha }}
+          source:  s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/variant_calling/
+          command: sync
+          destination: ./variant_calling
+          flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz"
+      - name: Upload file to Zenodo
+        uses: popperized/zenodo/upload@master
+        with:
+          secrets: ${{ secrets.ZENODO_API_TOKEN }}
+          parameters: |
+            {
+              ZENODO_DEPOSIT_ID = ""
+              ZENODO_UPLOAD_PATH = "./variant_calling"
+            }
+

conf/test_full_germline.config

@@ -18,7 +18,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'
 
     // Other params
-    tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'
+    tools                     = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
     split_fastq               = 50000000
     use_annotation_cache_keys = true
 }

conf/test_full_germline_wes.config

@@ -0,0 +1,25 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running full-size tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test_full_germline,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Full test profile for germline VC'
+    config_profile_description = 'Full test dataset to check germline VC pipeline function'
+
+    // Input data for full size test
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_Agilent_full_test.csv'
+
+    // Other params
+    intervals                 = 'https://zenodo.org/record/6513789/files/Agilent_v7.bed' //TODO: upload own intervals files prepended with "chr"
+    wes                       = true
+    tools                     = 'strelka,freebayes,haplotypecaller,deepvariant'
+    use_annotation_cache_keys = true
+}

nextflow.config

@@ -248,6 +248,7 @@ profiles {
     // Extra test profiles for full tests on AWS
     test_full                  { includeConfig 'conf/test_full.config' }
     test_full_germline         { includeConfig 'conf/test_full_germline.config' }
+    test_full_germline_wes     { includeConfig 'conf/test_full_germline_wes.config' }
     // Extra test profiles for more complete CI
     alignment_to_fastq         { includeConfig 'conf/test/alignment_to_fastq.config' }
     annotation                 { includeConfig 'conf/test/annotation.config' }