Short workflow for lineage analysis wastewater sars-cov-2 ampliconic data

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: /SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac.ga
+  testParameterFiles:
+  - /SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml
+  authors:
+  - name: Polina Polunina
+    orcid: 0000-0002-0507-460
+  - name: "B\xE9r\xE9nice 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/SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml

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+- doc: Test outline for SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac
+  job:
+    ARTIC primer scheme:
+      class: File
+      path: test-data/primers.bed
+      filetype: bed
+    VCF:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: sample1.fastq
+        path: test-data/VCF_sample1.fastq.vcf
+      - class: File
+        identifier: sample13.fastq
+        path: test-data/VCF_sample13.fastq.vcf
+    BAM collection of aligned and preprocessed reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: sample1.fastq
+        path: test-data/BAM collection of aligned and preprocessed reads_sample1.fastq.bam
+      - class: File
+        identifier: sample13.fastq
+        path: test-data/BAM collection of aligned and preprocessed reads_sample13.fastq.bam
+    Time(s) metadata CSV file:
+      class: File
+      path: test-data/csv_meta.csv
+      filetype: csv
+  outputs:
+    'Cojac: mutbamscan on input dataset(s): Mutation co-occurences':
+      asserts:
+        has_text:
+          text: "73_AY42"
+    '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"