Merge pull request #31 from galaxyproject/add-covid-consensus-wf

Add the covid-19 consensus workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/.dockstore.yml

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+version: 1.2
+workflows:
+- name: 'COVID-19-CONSENSUS-CONSTRUCTION'
+  primaryDescriptorPath: /consensus-from-variation.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /consensus-from-variation-test.yml

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md

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+0.1
+---------
+- Initial version of COVID-19: consensus construction

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/README.md

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+COVID-19: consensus construction
+--------------------------------
+
+This workflow aims at generating reliable consensus sequences from variant
+calls according to transparent criteria that capture at least some of the
+complexity of variant calling.
+
+It takes a collection of VCFs and a collection of the corresponding
+aligned reads (for the purpose of calculating genome-wide coverage) such as
+produced by any of the four variant calling workflows in
+https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling
+and generates a collection of viral consensus sequences and a multisample FASTA
+of all these sequences.
+
+Each consensus sequence is guaranteed to capture all called, filter-passing
+variants as defined in the VCF of its sample that reach a user-defined
+consensus allele frequency threshold.
+
+Filter-failing variants and variants below a second user-defined minimal
+allele frequency threshold will be ignored.
+
+Genomic positions of filter-passing variants with an allele frequency in
+between the two thresholds will be hard-masked (with N) in the consensus
+sequence of their sample.
+
+Genomic positions with a coverage (calculated from the read alignments input)
+below another user-defined threshold will be hard-masked, too, unless they are
+consensus variant sites.

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation-test.yml

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+- doc: Test consensus building from called variants
+  job:
+    Reference genome:
+      class: File
+      location: 'https://zenodo.org/record/4555735/files/NC_045512.2_reference.fasta?download=1'
+    aligned reads data for depth calculation:
+      class: Collection
+      collection_type: 'list'
+      elements:
+        - identifier: SRR11578257
+          class: File
+          path: test-data/aligned_reads_for_coverage.bam
+    Variant calls:
+      class: Collection
+      collection_type: 'list'
+      elements:
+        - identifier: SRR11578257
+          class: File
+          path: test-data/final_snpeff_annotated_variants.vcf
+  outputs:
+    multisample_consensus_fasta:
+      file: test-data/masked_consensus.fa
+