Add SameStr workflow

workflows/microbiome/samestr-workflow/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /samestrgal.ga
+  testParameterFiles:
+  - /samestrgal-tests.yml
+  authors:
+  - name: 'Xenia Morera Martínez'
+    orcid: 0009-0000-2380-8385

workflows/microbiome/samestr-workflow/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2026-06-18
+
+First release.

workflows/microbiome/samestr-workflow/README.md

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+# SamestrGal for shared-strain detection in metagenomes
+
+This workflow processes paired-end shotgun metagenomic sequencing reads from multiple samples. It performs the following steps:
+
+- **Preprocessing**: Quality trimming and host read removal using KneadData
+- **Taxonomic profiling and marker-based alignment**: MetaPhlAn4 or mOTUs for taxonomic classification and marker based alignment
+- **Strain detection**: SameStr tools identify strains across samples and compute pairwise strain comparisons using Maximum Variant Profile Similarity (MVS) scores.
+
+## Inputs
+
+- **Raw Reads**: A collection of paired-end FASTQ files from one or more samples to compare
+- **Run MetaPhlAn**: Boolean parameter (default: true) that enables MetaPhlAn-based strain detection
+
+## Outputs
+
+ - **MetaPhlAn results** (if enabled): SNV profile summary statistics, taxon counts, strain events, and co-occurrence tables

workflows/microbiome/samestr-workflow/samestrgal-tests.yml

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+- doc: Test outline for samestrgal
+  job:
+    Raw Reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        collection_type: paired
+        identifier: 28C
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/20745835/files/28C_R1.fastq.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/20745835/files/28C_R2.fastq.gz
+          filetype: fastqsanger.gz
+      - class: Collection
+        collection_type: paired
+        identifier: 28B
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/20745835/files/28B_R1.fastq.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/20745835/files/28B_R2.fastq.gz
+          filetype: fastqsanger.gz
+      - class: Collection
+        collection_type: paired
+        identifier: 28A
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/20745835/files/28A_R1.fastq.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/20745835/files/28A_R2.fastq.gz
+          filetype: fastqsanger.gz
+    Select Host reference genome: hg19
+    Select Sequencer for Trimmomatic: NexteraPE
+    Select MetaPhlAn Database: mpa_vJan25_CHOCOPhlAnSGB_202503-11062025
+    Select SameStr database: mpa_vJan25_CHOCOPhlAnSGB_202503-11062025
+    Run MetaPhlAn: true
+    "Percent identity": 0.9
+    "Minimum alignment length": 40
+    "Minimum base quality": 20
+    "Minimum alignment quality": 0
+    "Minimum vertical coverage": 3
+    "SameStr Filter: Minimum samples per clade": 2
+    "SameStr Filter: Marker truncation length": 50
+    "SameStr Filter: Nucleotides minimum variant coverage": 2
+    "SameStr Filter: Minimum variant coverage fraction": 0.05
+    "SameStr Filter: Minimum position coverage": 1
+    "SameStr Filter: Position coverage standard deviation cutoff": 3.0
+    "SameStr Filter: Minimum horizontal coverage": 5000
+    "SameStr Filter: Minimum sample coverage per position": 2
+    "SameStr Summarize: Minimum overlap for comparison": 5000
+    "SameStr Summarize: Minimum similarity for shared strains": 0.999
+  outputs:
+    "stats file":
+      element_tests:
+        t__SGB15299:
+          asserts:
+            - that: has_text
+              text: "28B"
+        t__SGB4285:
+          asserts:
+            - that: has_text
+              text: "28B"
+        t__SGB6362:
+          asserts:
+            - that: has_text
+              text: "28B"
+    "taxon counts":
+      asserts:
+        - that: has_text
+          text: "28A"
+        - that: has_text
+          text: "28B"
+        - that: has_text
+          text: "28C"
+    "strain events":
+      asserts:
+        - that: has_text
+          text: "t__SGB15299"
+        - that: has_text
+          text: "t__SGB4285"
+        - that: has_text
+          text: "t__SGB6362"
+        - that: has_text
+          text: "28B"
+        - that: has_text
+          text: "28C"
+    "cooccurrences":
+      asserts:
+        - that: has_text
+          text: "28A"
+        - that: has_text
+          text: "28B"
+        - that: has_text
+          text: "28C"