Interview-Driven Workflow Construction and Repair in Galaxy

IWC Comparison Notes: Ebola Virus Infection RNA-seq Analysis

Nearest Exemplar Identification

Primary Domain Exemplar (Differential Expression): transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting
Secondary Domain Exemplar (Paired-end Collection Mapping & Quantification): transcriptomics/rnaseq-pe/rnaseq-pe
Confidence: High (matching domain: transcriptomics/RNA-seq, matching collection topology: list:paired mapped to per-sample quantification tables and reduced into DESeq2).

Relevant Subgraph Excerpt

Excerpt from transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting (iwc-exemplar.gxwf.yml):

  - id: Differential Analysis
    label: Differential Analysis
    tool_id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3
    tool_version: 2.11.40.8+galaxy3
    in:
      - id: select_data|rep_factorName_0|rep_factorLevel_0|countsFile
        source: Counts from changed condition
      - id: select_data|rep_factorName_0|rep_factorLevel_1|countsFile
        source: Counts from reference condition
    out:
      - id: deseq_out
      - id: plots
      - id: counts_out
    tool_state:
      output_options:
        output_selector:
          - pdf
          - normCounts

Structural Comparison & Diff

Feature	Upstream Briefs (`ebola-test`)	IWC Exemplar (`rnaseq-de` / `rnaseq-pe`)	Comparison & Guidance
Input Collection Shape	`list:paired` (FASTQ)	`list:paired` (`rnaseq-pe`)	Direct match. Preserves sample names across map-over operations.
Quantification Tier	Salmon pseudoalignment (`salmon quant`)	HISAT2/STAR + featureCounts	Distinct tool family (Salmon vs aligner+counter), but topologically identical: map over `list:paired` producing a list of sample tabular files.
Differential Expression	Multi-factor DESeq2 (WT vs KO, Mock vs Ebola, 24 vs 48 HPI)	Two-condition DESeq2 (`rnaseq-de`)	The exemplar uses pairwise factor levels. In the multi-factor setting, DESeq2 takes the sample matrix or factor levels across conditions.
Outputs	`quant.sf` collection, normalized counts, differential results, diagnostic plots	Normalized counts, differential results, volcano/heatmap plots	Consistent output hierarchy; promoting `salmon_quant_collection` as a checkpoint output follows IWC best practices.

Guidance for Downstream Template Authoring

Draft Steps:
- salmon_quant: Drafty step marked with _plan_tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon mapped over reads_paired_collection.
- deseq2: Drafty step marked with _plan_tool_id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2 connected to the salmon_quant collection output and metadata tables.
Collection Wiring: Use connect_across: true or native Galaxy collection mapping semantics so that Salmon operates per sample pair and passes a list collection into DESeq2.