Add MAG Genome Annotation Parallel wf (#1124)

* Add MAG Genome Annotation Parallel wf

* turn off bakta

* try different file as input

* fix test

* change assert for one output

* Update workflows/microbiome/mag-genome-annotation-parallel/MAG-Genome-Annotation-Parallel-tests.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* review changes

* Update workflows/microbiome/mag-genome-annotation-parallel/MAG-Genome-Annotation-Parallel.ga

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update workflows/microbiome/mag-genome-annotation-parallel/README.md

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

* Update workflows/microbiome/mag-genome-annotation-parallel/README.md

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: paulzierep <paul.zierep@googlemail.com>

Author: 3 people

workflows/microbiome/mag-genome-annotation-parallel/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /MAG-Genome-Annotation-Parallel.ga
+  testParameterFiles:
+  - /MAG-Genome-Annotation-Parallel-tests.yml
+  authors:
+  - name: Paul Zierep
+    orcid: 0000-0003-2982-388X

workflows/microbiome/mag-genome-annotation-parallel/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2026-03-01
+
+- First release

workflows/microbiome/mag-genome-annotation-parallel/MAG-Genome-Annotation-Parallel-tests.yml

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+- doc: Test outline for MAG-Genome-Annotation-Parallel
+  job:
+    Bacterial Genomes:
+      class: Collection
+      collection_type: list
+      elements:
+        - class: File
+          identifier: 50contig_reads_binette_bin1.fasta
+          location: https://zenodo.org/records/18635101/files/50contig_reads_binette_bin2.fasta
+    Plasmid detection database: plasmidfinder_1307168_2019_08_28
+    Bacterial genome annotation database: V5.0_2023-02-20
+    AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2
+    Run Bakta: true
+  outputs:
+    multiqc html report:
+      asserts:
+      - that: has_text
+        text: "50contig_reads_bin"
+    ISEScan Merged Output:
+      asserts:
+      - that: has_n_lines
+        n: "0"
+    Integron Finder Merged Output:
+      asserts:
+      - that: has_n_lines
+        n: "0"
+    bakta cut annotation summary:
+      asserts:
+      - that: has_n_lines
+        n: "16"
+      - that: has_n_columns
+        n: "2"
+    PlasmidFinder Merged Summary:
+      asserts:
+      - that: has_text
+        text: "Sample	Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number"
+      - that: has_n_lines
+        n: 1