Add simple diploid variant calling workflow

workflows/variant-calling/simple-diploid-variant-calling/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Simple-variant-calling-for-diploid-taxa.ga
+  testParameterFiles:
+  - /Simple-variant-calling-for-diploid-taxa-tests.yml
+  authors:
+  - name: Anton Nekrutenko
+    orcid: 0000-0002-5987-8032

workflows/variant-calling/simple-diploid-variant-calling/CHANGELOG.md

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+# Changelog
+
+## [0.1.0] - 2025-10-25
+
+- Initial version of simple variant calling workflow for diploid taxa

workflows/variant-calling/simple-diploid-variant-calling/README.md

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+# Simple variant calling for diploid taxa
+
+Performs variant analysis on paired-end Illumina reads against a reference genome. The workflow uses BWA-MEM for read mapping and FreeBayes for variant calling.
+
+## Inputs
+
+- Paired-end Illumina reads (fastqsanger format)
+- Reference genome
+
+## Outputs
+
+- VCF file with called variants
+- Quality control reports for preprocessing and mapping
+
+## Processing
+
+- Adapter trimming and quality filtering with fastp
+- Read mapping with BWA-MEM
+- Alignment filtering to retain only properly paired reads mapped in proper orientation
+- PCR duplicate removal with Picard MarkDuplicates
+- Variant calling with FreeBayes

workflows/variant-calling/simple-diploid-variant-calling/Simple-variant-calling-for-diploid-taxa-tests.yml

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+- doc: Test outline for Simple-variant-calling-for-diploid-taxa
+  job:
+    Paired Collection:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: U0b_A_L2
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/17443317/files/Paired%20Collection_forward.fastqsanger.gz?download=1
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/17443317/files/Paired%20Collection_reverse.fastqsanger.gz?download=1
+    Reference genome: hg38
+  outputs:
+    Freebayes VCF:
+      asserts:
+      - has_text:
+          text: "chr11	8172157	.	GTG	GG"
+      - has_n_lines:
+          n: 804