VGP Precuration - Creation of the workflow to generate jbrowse2 instances with related species

workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Precuration-Jbrowse-tracks-alignments.ga
+  testParameterFiles:
+  - /Precuration-Jbrowse-tracks-alignments-tests.yml
+  authors:
+  - name: Patrik Smeds
+    orcid: 0000-0001-6228-2785
+  - name: Delphine Lariviere
+    orcid: 0000-0001-6421-3484

workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2026-05-07
+
+- Initial release: workflow generates JBrowse2 instances with assembly tracks (telomeres, gaps, coverage, optional gene annotation) and related-species alignments to assist manual curation of genome assemblies. Supports single- or dual-haplotype inputs.

workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml

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+# Planemo test configuration for Jbrowse2 Precuration tracks workflow
+# Test 1: Single haplotype with related species, no gene annotation
+# Test 2: Two haplotypes with related species and gene annotation
+#
+# All test files are hosted on Zenodo record 20074725. The Q_telomeres input
+# in the test reuses the P_telomeres file because the actual Q_telomeres test
+# file is empty and cannot be uploaded to Zenodo.
+
+- doc: Test 1 - Single haplotype, related species, no gene annotation
+  job:
+    Species Name: Test_species
+    Assembly Name: toLID
+    Haplotype 1:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Haplotype_1.fasta
+      filetype: fasta
+      hashes:
+      - hash_function: SHA-1
+        hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212
+    Related Species:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Related_species_1
+        location: https://zenodo.org/records/20074725/files/Related_species_1.fasta.gz
+        filetype: fasta.gz
+        hashes:
+        - hash_function: SHA-1
+          hash_value: 5121b574218ce9295fa6de1dd3fbdb1cfb9c68b1
+      - class: File
+        identifier: Related_species_2
+        location: https://zenodo.org/records/20074725/files/Related_species_2.fasta.gz
+        filetype: fasta.gz
+        hashes:
+        - hash_function: SHA-1
+          hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f
+    Telomere P:
+      class: File
+      location: https://zenodo.org/records/20074725/files/P_telomeres.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d
+    Telomere Q:
+      class: File
+      location: https://zenodo.org/records/20074725/files/P_telomeres.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d
+    Gaps:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Gaps.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 5a14e6a11d9dc0ac41c3466f0693823a3f2c10be
+    Coverage:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Coverage.bigwig
+      filetype: bigwig
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4
+  outputs:
+    JBrowse2 Single Haplotype:
+      asserts:
+        has_text:
+          text: "JBrowse"
+    JBrowse2 Single Haplotype with related species:
+      element_tests: {}
+    JBrowse2 Single Haplotype with related species and Gene Tracks:
+      element_tests: {}
+
+- doc: Test 2 - Two haplotypes, related species, with gene annotation
+  job:
+    Species Name: Test_species
+    Assembly Name: toLID
+    Haplotype 1:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Haplotype_1.fasta
+      filetype: fasta
+      hashes:
+      - hash_function: SHA-1
+        hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212
+    Haplotype 2:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Haplotype_2.fasta
+      filetype: fasta
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 166cb118625113e39593bedb10aaea028c20f77d
+    Related Species:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Related_species_1
+        location: https://zenodo.org/records/20074725/files/Related_species_1.fasta.gz
+        filetype: fasta.gz
+        hashes:
+        - hash_function: SHA-1
+          hash_value: 5121b574218ce9295fa6de1dd3fbdb1cfb9c68b1
+      - class: File
+        identifier: Related_species_2
+        location: https://zenodo.org/records/20074725/files/Related_species_2.fasta.gz
+        filetype: fasta.gz
+        hashes:
+        - hash_function: SHA-1
+          hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f
+    Genes:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Compleasm_genes_track.gff
+      filetype: gff3
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 526abf443cc04c3904c2b2b140b19bb4f17622d0
+    Telomere P:
+      class: File
+      location: https://zenodo.org/records/20074725/files/P_telomeres.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d
+    Telomere Q:
+      class: File
+      location: https://zenodo.org/records/20074725/files/P_telomeres.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d
+    Gaps:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Gaps.bed
+      filetype: bed
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 5a14e6a11d9dc0ac41c3466f0693823a3f2c10be
+    Coverage:
+      class: File
+      location: https://zenodo.org/records/20074725/files/Coverage.bigwig
+      filetype: bigwig
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4
+  outputs:
+    JBrowse2 Hap1 vs Hap2 with gene tracks:
+      asserts:
+        has_text:
+          text: "JBrowse"
+    JBrowse2 Hap1 and hap2 with related species:
+      element_tests: {}
+    JBrowse2 Hap1 and hap2 with related species and gene tracks:
+      element_tests: {}