Add viral detection from bulk metagenomes

workflows/microbiome/viral-detection-from-bulk-metagenomes/.dockstore.yml

@@ -0,0 +1,12 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /viral-detection-from-bulk-metagenomes.ga
+  testParameterFiles:
+  - /viral-detection-from-bulk-metagenomes-test.yml
+  authors:
+  - name: Mina Hojat Ansari
+    orcid: 0000-0002-3602-7884
+  - name: "Niklas Stahl"

workflows/microbiome/viral-detection-from-bulk-metagenomes/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## [1.0] - 2026-26-04
+
+- First release

workflows/microbiome/viral-detection-from-bulk-metagenomes/README.md

@@ -0,0 +1,81 @@
+# Viral detection from bulk metagenomes
+
+## Overview
+
+This workflow identifies viral contigs from metagenomic assemblies using **geNomad** and performs downstream analyses including **taxonomy**, **functional annotation**, **binning**, **host prediction**, and **coverage estimation**.
+
+---
+
+## Inputs
+
+- **Assembled contigs** (FASTA, collection)
+- **Trimmed paired-end reads** (list:paired)
+
+### Requirements
+
+- Reads must be quality-controlled (trimmed, adapters removed)
+- Host contamination should be removed
+
+---
+
+## Workflow steps
+
+### 1. Viral contig prediction
+Viral sequences are identified from assembled contigs using **geNomad**.
+
+### 2. Provirus detection and refinement
+**CheckV** is used to identify proviruses. Extracted proviruses are re-analysed with **geNomad**.
+
+### 3. Merging viral predictions
+Viral contigs from both geNomad runs are combined.
+
+### 4. Clustering and dereplication
+Redundant sequences are removed using **MMseqs2** clustering.
+
+### 5. Quality assessment and filtering
+**CheckV** is used to assess sequence quality. Only sequences classified as:
+
+- Complete  
+- High-quality  
+- Medium-quality  
+
+are retained for downstream analysis.
+
+### 6. Host prediction
+Viral contigs are analysed using **iPHoP**.
+
+### 7. Functional annotation
+Viral genomes are annotated using **Pharokka**.
+
+### 8. Coverage estimation
+Reads are mapped using **Bowtie2** and coverage is calculated with **CoverM**.
+
+### 9. Viral genome binning (vMAGs)
+Viral contigs and coverage profiles are used by **vRhyme** to recover viral genomes.
+
+---
+
+## Outputs
+
+- Viral contigs (geNomad)
+- Taxonomy annotations
+- Gene annotations
+- Nonredundant viral sequences
+- CheckV quality reports
+- Filtered viral contigs
+- Host predictions (iPHoP)
+- Functional annotations (Pharokka)
+- Coverage table (CoverM)
+- vMAG bins (vRhyme)
+
+---
+
+## Notes
+
+- Only **medium- and high-quality sequences** are used for biological interpretation
+
+---
+
+## License
+
+MIT License

workflows/microbiome/viral-detection-from-bulk-metagenomes/viral-detection-from-bulk-metagenomes-test.yml

@@ -0,0 +1,112 @@
+- doc: Test for viral-detection-from-bulk-metagenomes
+  job:
+    Assembled contigs:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: SRR24759598
+        location: https://zenodo.org/records/19831629/files/SRR24759598.fasta
+      - class: File
+        identifier: SRR24759616
+        location: https://zenodo.org/records/19831629/files/SRR24759616.fasta
+    Trimmed reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: SRR24759598
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/19831629/files/SRR24759598_forward.fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/19831629/files/SRR24759598_reverse.fastqsanger.gz
+      - class: Collection
+        type: paired
+        identifier: SRR24759616
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/19831629/files/SRR24759616_forward.fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/19831629/files/SRR24759616_reverse.fastqsanger.gz
+  outputs:
+    output cluster:
+      asserts:
+      - that: has_n_lines
+        n: 315
+        delta: 10
+    quality summary:
+      asserts:
+      - that: has_n_lines
+        n: 300
+        delta: 10
+    complete genomes:
+      asserts:
+      - that: has_n_lines
+        n: 2
+        delta: 1
+      - that: has_text
+        text: "contig_id"
+    coverage:
+      asserts:
+      - that: has_n_lines
+        n: 6
+        delta: 1
+      - that: has_text
+        text: "Contig"
+    output seqs:
+      asserts:
+      - that: has_size
+        size: 776500
+        delta: 50000
+    best bins membership:
+      asserts:
+      - that: has_n_lines
+        n: 0
+    best bins summery:
+      asserts:
+      - that: has_n_lines
+        n: 0
+    coverage file:
+      asserts:
+      - that: has_n_lines
+        n: 83
+        delta: 10
+      - that: has_text
+        text: "scaffold"
+    pharokka gbk:
+      asserts:
+      - that: has_size
+        size: 557600
+        delta: 50000
+    pharokka gff:
+      asserts:
+      - that: has_size
+        size: 342800
+        delta: 50000
+    genomad fasta:
+      element_tests:
+        SRR24759616:
+          asserts:
+          - that: has_size
+            value: 434300
+            delta: 50000
+    bam for vRhyme:
+      element_tests:
+        SRR24759616:
+          asserts:
+          - that: has_size
+            value: 65500
+            delta: 5000
+    bam for CoverM:
+      element_tests:
+        SRR24759616:
+          asserts:
+          - that: has_size
+            value: 24900
+            delta: 5000