# RNAflow Galaxy-native RNA-seq reproduction

## Summary

This entry reproduces the human RNA-seq test data from `hoelzer-lab/rnaflow` in Galaxy using the same core analysis stages: FastQC, HISAT2, featureCounts, and DESeq2. The public Galaxy history is the primary artifact.

## Run Snapshot

Target: `hoelzer-lab/rnaflow` at source ref `f2d26a3418adc10d24b5042ad653081a9500245b`.

Public/importable Galaxy history: [RNAflow real-world GitHub reproduction 2026-05-27](https://usegalaxy.org/histories/view?id=bbd44e69cb8906b529dc497e1d783b61).

Validation status: pass with warnings. The controlled website status is `warning` because the result is a useful Galaxy-native reproduction with documented caveats.

## Source

- Type: github_repository
- URL: https://github.com/hoelzer-lab/rnaflow
- Reference: f2d26a3418adc10d24b5042ad653081a9500245b
- Data: `test-data/hsa`
- Samples: four single-end FASTQ files, two `MAQCA` replicates and two `MAQCB` replicates

## Galaxy Reproduction

- History: https://usegalaxy.org/histories/view?id=bbd44e69cb8906b529dc497e1d783b61
- Public: yes
- Importable: yes
- Execution surface: galaxy-cli+galaxy-api-fallback
- Galaxy instance: https://usegalaxy.org
- Galaxy history id: `bbd44e69cb8906b529dc497e1d783b61`

## What Ran

- Uploaded the RNAflow `test-data/hsa` FASTQs and DESeq2 sample sheet.
- Ran FastQC on all four samples.
- Ran HISAT2 against the built-in `hg38` reference.
- Ran featureCounts with the built-in `hg38` annotation, single-end unstranded mode.
- Ran DESeq2 for `MAQCB` compared with reference `MAQCA`.

## Key Metrics

- FASTQ samples: 4, each with 100000 reads.
- HISAT2 overall alignment rate: 79.60% to 80.59%.
- featureCounts assigned reads: 62228 to 62675.
- DESeq2 raw rows: 28395.
- DESeq2 finite rows after removing filtered `NA` statistics: 6744.
- DESeq2 genes with adjusted p-value below 0.05: 979.

## Validation

- Status: warning
- Profile: rnaseq_differential_expression

The status is `warning` rather than `pass` because this is a Galaxy-native reproduction of the RNAflow test workflow, not an exact Nextflow/conda execution of RNAflow itself. HISAT2 and DESeq2 were submitted through a narrow direct Galaxy API fallback during the run because the installed `galaxy-cli` did not yet normalize nested data input payloads for those wrappers.

## Files

- Metadata: `metadata.yaml`
- Validation report: `validation_report.json`
- Provenance: `provenance.json`

The original run also produced a `run_summary.md`; this page carries the reviewer-facing run summary while the validation report carries the machine-readable checks and metrics.

Entry id: `wf_20260527_rnaflow-galaxy-native-rnaseq-reproduction`