wip: lexicmap and logan workflows w download

workflows/data-fetching/kmindex-logan-sra-retrieval/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /kmindex-logan-sra-retrieval.ga
+  testParameterFiles:
+  - /kmindex-logan-sra-retrieval-tests.yml
+  authors:
+  - name: Danielle Callan
+    orcid: 0009-0009-3690-8372

workflows/data-fetching/kmindex-logan-sra-retrieval/CHANGELOG.md

@@ -0,0 +1,17 @@
+# Changelog
+
+## [0.1] - 2026-04-16
+
+### Added
+
+- Initial release of KMIndex / Logan SRA Hit Retrieval workflow
+- K-mer based sequence search against Logan unitig indexes
+- Automatic SRA accession identification from search results
+- Parallel download of matching SRA runs
+- Separate outputs for paired-end and single-end reads
+- Configurable search parameters:
+  - Minimum shared k-mer proportion (default: 0.5)
+  - Z-value for k-mer extension sensitivity (default: 6)
+  - Maximum number of hits to download
+- Comprehensive workflow documentation in README
+- Test suite with sample query sequence

workflows/data-fetching/kmindex-logan-sra-retrieval/README.md

@@ -0,0 +1,56 @@
+# KMIndex / Logan SRA Hit Retrieval
+
+## Overview
+
+Search a query sequence against a KMIndex/Logan index and rapidly download matching SRA runs into your Galaxy history.
+
+This workflow uses k-mer–based matching for fast identification of highly similar sequences.
+
+## Inputs
+
+- **Query sequence** (FASTA) — nucleotide sequence to search
+- **Index to query** — KMIndex/Logan database to search against
+- **Max hits to download** — maximum number of SRA runs to retrieve
+- **Minimum shared k-mer proportion** (0.0–1.0, default: 0.5) — threshold for match inclusion
+- **Z-value** (k-mer extension factor, default: 6) — controls k-mer matching sensitivity
+
+## Outputs
+
+- **Accession list** (TXT) — list of downloaded SRA IDs
+- **Paired-end reads** (collection) — paired FASTQ files from matching runs
+- **Single-end reads** (collection) — single FASTQ files from matching runs
+
+## Parameter Tips
+
+**More stringent** (fewer, closer matches):
+- ↑ shared k-mer proportion
+
+**More permissive** (more, broader matches):
+- ↓ shared k-mer proportion
+
+**Z-value**:
+- Higher → more specific, may miss distant matches
+- Lower → more sensitive, may include weaker matches
+
+## When to Use KMIndex / Logan
+
+Use this workflow when you need:
+- Fast searches at scale
+- Exact or near-exact matches
+- Minimal parameter tuning
+
+Use the LexicMap workflow if you need:
+- Approximate matching (mismatches/gaps)
+- Sensitivity to divergent sequences
+- BLAST-like alignment scoring
+
+## Rule of thumb
+
+- High similarity → use KMIndex / Logan
+- Unknown or divergent sequences → use LexicMap
+
+## Notes
+
+- Designed for speed; less sensitive to divergent sequences than alignment-based methods
+- Very low thresholds may return weak or spurious matches
+- Outputs are split into paired-end and single-end collections for downstream use

workflows/data-fetching/kmindex-logan-sra-retrieval/kmindex-logan-sra-retrieval-tests.yml

@@ -0,0 +1,20 @@
+- doc: Test KMIndex/Logan SRA retrieval with query sequence
+  job:
+    Query Sequence:
+      class: File
+      path: test-data/query-sequence.fasta
+      hashes:
+      - hash_function: SHA-1
+        hash_value: 69b9d3d941720ef225f5545a711e9ab8a209da49
+    Index To Query: "VIRALRNA_ROD"
+    Z-value (k-mer extension factor): 6
+    Minimum shared k-mer proportion: 0.5
+    How many accessions to keep: 5
+  outputs:
+    KMIndex/ Logan Matching Accessions List:
+      file: test-data/expected-accession-list.txt
+      compare: contains
+    Paired End Reads:
+      class: Collection
+    Single End Reads:
+      class: Collection