Merge pull request galaxyproject#17 from mvdbeek/covid_workflow_wolfgang

Add pe-illumina-wgs workflow

.github/workflows/workflow_test.yml

@@ -206,6 +206,7 @@ jobs:
       run: |
         git config --global user.email "[email protected]"
         git config --global user.name "$GITHUB_USER"
+        git config --global init.defaultBranch main
     - uses: fusion-engineering/setup-git-credentials@v2
       with:
         credentials: 'https://${{ env.GITHUB_USER }}:${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}@github.com/'

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/.dockstore.yml

@@ -0,0 +1,7 @@
+version: 1.2
+workflows:
+- name: 'COVID-19-PE-WGS-ILLUMINA'
+  primaryDescriptorPath: /pe-wgs-variation.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /pe-wgs-variation-test.yml

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md

@@ -0,0 +1,3 @@
+0.1
+---------
+- Initial version of COVID-19: variation analysis on WGS PE data workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/README.md

@@ -0,0 +1,6 @@
+COVID-19: variation analysis on WGS PE data
+-------------------------------------------
+
+This workflows performs paired end read mapping with bwa-mem followed by
+sensitive variant calling across a wide range of AFs with lofreq and variant
+annotation with snpEff 4.5covid19.

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation-test.yml

@@ -0,0 +1,27 @@
+- doc: Test workflow execution using paired end illumina accession
+  job:
+    NC_045512.2 FASTA sequence of SARS-CoV-2:
+      class: File
+      path: test-data/NC_045512.2.fasta
+    Paired Collection:
+      class: Collection
+      collection_type: 'list:paired'
+      elements:
+        - class: Collection
+          type: paired
+          identifier: SRR11578257
+          elements:
+          - identifier: forward
+            class: File
+            location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R1.fq.gz"
+          - identifier: reverse
+            class: File
+            location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R2.fq.gz"
+  outputs:
+    annotated_variants:
+      attributes: {}
+      element_tests:
+        SRR11578257:
+          path: test-data/final_snpeff_annotated_variants.vcf
+          compare: diff
+          lines_diff: 6