Metagenomic raw reads analysis workflow without assembly

workflows/microbiome/metagenomic-raw-reads-amr-analysis/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /metagenomic-raw-reads-amr-analysis.ga
+  testParameterFiles:
+  - /metagenomic-raw-reads-amr-analysis-tests.yml
+  authors:
+  - name: ABRomics
+    email: [email protected]
+  - name: abromics-consortium
+    url: https://www.abromics.fr/
+  - name: Hugo Lefeuvre
+    orcid: 0009-0005-6834-4058

workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md

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+# Changelog
+
+## [1.0] - 2025-11-12
+
+- First release

workflows/microbiome/metagenomic-raw-reads-amr-analysis/README.md

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+# Raw reads AMR analysis from metagenomic data
+
+This workflow generates functional and taxonomic information from paired short reads.
+
+## Raw reads Annotation
+
+Directly from trimmed raw reads, following processing steps are performed:
+
+* **Taxonomic Assignment** using Sylph and Sylph-tax
+* **AMR detection** with Groot and deepARG
+* **Results uniformization** with argNorm
+
+## Input Requirements
+
+Input reads must be quality-filtered, with host reads removed.
+
+* **Trimmed reads** : Quality-trimmed reads from individual samples, used solely for abundance estimation.

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis-tests.yml

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+- doc: Test outline for metagenomic-raw-reads-amr-analysis workflow
+  job:
+    Metagenomics Trimmed reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: raw_reads_metag_test
+        elements:
+          - class: File
+            identifier: forward
+            location: https://zenodo.org/records/17395554/files/PSM6XBT3_500k_R1.fastq.gz
+          - class: File
+            identifier: reverse
+            location: https://zenodo.org/records/17395554/files/PSM6XBT3_500k_R2.fastq.gz
+    Sylph database: sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb
+    Sylph tax database: sylph_tax_downloaded_08112025
+    DeepARG database: deeparg_1.0.4-07112025
+    Groot database: arg-annot.90-1.1.2-08112025
+    Groot database for ARGnorm: groot-argannot
+    Deeparg minimum probability for considering a reads as ARG-like: '0.8'
+    Groot average base pair length of reads: '100'
+    Groot coverage cutoff for reporting ARGs: '0.6'
+  outputs:
+    Sylph Taxonomy Profiling:
+      element_tests:
+        raw_reads_metag_test:
+          has_text:
+            text: "Taxonomic_abundance"
+          has_n_columns:
+            n: 15
+    Sylph Taxonomy Profiling:
+      element_tests:
+        raw_reads_metag_test:
+          has_text:
+            text: "clade_name"
+          has_n_columns:
+            n: 2
+    DeepARG Mapping ARG:
+      element_tests:
+        raw_reads_metag_test:
+          has_text:
+            text: "#ARG"
+          has_n_columns:
+            n: 4
+    Groot Report:
+      element_tests:
+        raw_reads_metag_test:
+          asserts:
+            has_text:
+              text: "argannot~~~(Bla)cfxA2~~~AF504910:1-966"
+            has_n_columns:
+              n: 4
+    argNorm Groot Report:
+      element_tests:
+        raw_reads_metag_test:
+          asserts:
+            has_text:
+              text: "ARO:3003002"
+            has_n_columns:
+              n: 2
+    argNorm DeepARG Report:
+      element_tests:
+        raw_reads_metag_test:
+          has_text:
+            text: "#ARG"
+          has_n_columns:
+            n: 4
+    Tooldistillator Summarize:
+      element_tests:
+        raw_reads_metag_test:
+          asserts:
+            - that: has_text
+              text: "groot_report"
+            - that: has_text
+              text: "sylph_report"
+            - that: has_text
+              text: "sylphtax_report"
+            - that: has_text
+              text: "argnorm_report"
+            - that: has_text
+              text: "deeparg_report"
+            - that: has_text
+              text: "sylph-tax.sylphmpa_file"