Adding a Microbiome Workflow PathoGFAIR

workflows/microbiome/PathoGFAIR/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /PathoGFAIR.ga
+  testParameterFiles:
+  - /PathoGFAIR-tests.yml
+  authors:
+  - name: Engy Nasr
+    orcid: 0000-0001-9047-4215
+  - name: "Bérénice Batut"
+    orcid: 0000-0001-9852-1987
+  - name: Paul Zierep
+    orcid: 0000-0003-2982-388X

workflows/microbiome/PathoGFAIR/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-07-03
+
+First release.

workflows/microbiome/PathoGFAIR/PathoGFAIR-tests.yml

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+- doc: Test outline for PathoGFAIR
+  job:
+    reference_genome_of_tested_pathogen_strain:
+      class: File
+      location: https://zenodo.org/record/12190648/files/reference_genome_of_tested_strain.fasta.gz
+      filetype: fasta.gz
+    collection_of_all_samples:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: collection_of_all_samples_Spike3bBarcode10
+        location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode10.fastq.gz
+        filetype: fastqsanger.gz
+      - class: File
+        identifier: collection_of_all_samples_Spike3bBarcode12
+        location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode12.fastq.gz
+        filetype: fastqsanger.gz
+    samples_profile: map-pb
+    kraken_database: k2_minusb_20210517
+    host_reference_genome: apiMel3
+  outputs:
+    heatmap_table:
+      attributes: {}
+      path: test-data/heatmap_table.tabular