add new workflow for WW sars-cov-2 amliconic analysis

workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data.ga
+  testParameterFiles:
+  - /WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data-tests.yml
+  authors:
+  - name: Polina Polunina
+    orcid: 0000-0002-0507-460
+  - name: "Bérénice Batut"
+    orcid: 0000-0001-9852-198
+  - name: Wolfgang Maier
+    orcid: 0000-0002-9464-664

workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/CHANGELOG.md

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+# Changelog
+
+## [0.1]
+
+- Initial version of COVID-19: variation analysis on ARTIC PE data workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/README.md

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+SARS-CoV-2 wastewater surveillance: lineages analysis on ARTIC PE data
+---------------------------------------------
+
+The workflow for SARS-CoV-2 wastewater Illumina-sequenced ARTIC data analysis

workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data-tests.yml

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+- doc: Test outline for WW-SARS-CoV-2:-lineages-analysis-on-ARTIC-PE-data
+  job:
+    NC_045512.2 FASTA sequence of SARS-CoV-2:
+      class: File
+      path: test-data/NC_045512.2 FASTA sequence of SARS-CoV-2.fasta
+      filetype: fasta
+    ARTIC primer BED:
+      class: File
+      path: test-data/ARTIC primer BED.bed
+      filetype: bed
+    ARTIC primers to amplicon assignments:
+      class: File
+      path: test-data/ARTIC primers to amplicon assignments.bed
+      filetype: bed
+    BED defining amplicons for COJAC:
+      class: File
+      path: test-data/BED defining amplicons for COJAC.bed
+      filetype: bed
+    Paired Collection:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: sample1.fastq
+        elements:
+        - class: File
+          identifier: forward
+          path: test-data/Paired Collection_forward.fastqsanger.gz
+        - class: File
+          identifier: reverse
+          path: test-data/Paired Collection_reverse.fastqsanger.gz
+      - class: Collection
+        type: paired
+        identifier: sample13.fastq
+        elements:
+        - class: File
+          identifier: forward
+          path: test-data/Paired Collection_forward.fastqsanger.gz
+        - class: File
+          identifier: reverse
+          path: test-data/Paired Collection_reverse.fastqsanger.gz
+  outputs:
+    'Cojac: mutbamscan on input dataset(s): Mutation cooccurrence (yaml)':
+      element_tests:
+        sample1.fastq:
+          asserts:
+            has_text:
+              text: "73_AY42"
+        sample13.fastq:
+          asserts:
+            has_text:
+              text: "76_BA1"
+    'Freyja: Demix on input dataset(s): Lineages abundances summary':
+      element_tests:
+        sample1.fastq:
+          asserts:
+            has_text:
+              text: "Omicron"
+        sample13.fastq:
+          asserts:
+            has_text:
+              text: "summarized"