add align, chain, and net workflow

workflows/genome-alignment/align-chain-net/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /align.ga
+  testParameterFiles:
+  - /align-tests.yml
+  authors:
+  - name: Penn State University
+    url: https://www.ccbb.psu.edu/
+  - name: "Martin Čech"
+    orcid: 0000-0002-9318-1781

workflows/genome-alignment/align-chain-net/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2025-04-28
+
+Initial version of the genome align, chain, and net workflow with kegalign, lastz, and UCSC tools.

workflows/genome-alignment/align-chain-net/README.md

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+# Genome align, chain, and net workflow with KegAlign, lastz, and UCSC tools
+
+This workflow is designed for alignment of two large (e.g. mammalian) genomes with expected divergence ranging from 1 to 40%. It uses a GPU-accelerated version of lastz (KegAlign) -- this means a machine with a GPU is required for the step with the KegAlign tool.

workflows/genome-alignment/align-chain-net/align-tests.yml

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+- doc: Test net generation for caeJap1 vs ce11 alignment
+  job:
+    TARGET_fasta_index:
+      class: File
+      path: test-data/ce11.fa.fai
+    QUERY_fasta_index:
+      class: File
+      path: test-data/caeJap1.fa.fai
+    TARGET_Sequence:
+      class: File
+      location: https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.fa.gz
+    QUERY_Sequence:
+      class: File
+      location: https://hgdownload.soe.ucsc.edu/goldenPath/caeJap1/bigZips/caeJap1.fa.gz
+  outputs:
+    netfilter_out:
+      class: File
+      path: test-data/filtered_net.ucsc.net