pass
public, importable
| id | wf_20260523_intro-to-dge-deseq2-reproduction |
|---|
| workflow_class | rnaseq_differential_expression |
|---|
| validation_profile | rnaseq_differential_expression |
|---|
| validation_status | pass |
|---|
| review_status | draft |
|---|
| source_type | github_repository |
|---|
| source_ref | 190d303ad44c33d2d64e013ebe34837e73c3f332 |
|---|
| source_url | https://github.com/hbctraining/Intro-to-DGE |
|---|
| galaxy_instance | https://usegalaxy.org |
|---|
| galaxy_history_id | bbd44e69cb8906b520c2ac86da470003 |
|---|
| execution_surface | galaxy-cli |
|---|
| created | 2026-05-23 |
|---|
| updated | 2026-05-23 |
|---|
| tags | rnaseq, differential-expression, deseq2, galaxy-cli |
|---|
Entry README
Intro to DGE DESeq2 reproduction
Summary
Galaxy CLI reproduction of the Intro-to-DGE count-matrix differential-expression workflow with DESeq2 and bioartifact validation.
Source
- Type: github_repository
- URL: https://github.com/hbctraining/Intro-to-DGE
- Reference: 190d303ad44c33d2d64e013ebe34837e73c3f332
Galaxy Reproduction
- History: https://usegalaxy.org/histories/view?id=bbd44e69cb8906b520c2ac86da470003
- Public: yes
- Importable: yes
- Execution surface: galaxy-cli
Validation
- Status: pass
- Profile: rnaseq_differential_expression
Files
- Metadata: `metadata.yaml`
- Validation report: `validation_report.json`
- Provenance: `provenance.json`
Entry id: `wf_20260523_intro-to-dge-deseq2-reproduction`
Validation Summary
| Status | pass |
|---|
| Profile | rnaseq_differential_expression |
|---|
| Checks | 7 |
|---|
Checks
| Name | Status | Details |
|---|
| galaxy_history_created | pass | {"details": {"history_id": "bbd44e69cb8906b520c2ac86da470003"}} |
| inputs_uploaded | pass | {"details": {"sample_count": 8, "sample_sheet_id": "f9cad7b01a4721351085ab574fafdb35"}} |
| collection_order | pass | {"details": {"collection_id": "1bc813c15642b5fd", "sample_order": ["KO1", "KO2", "KO3", "KO4", "WT1", "WT2", "WT3", "WT4"]}} |
| deseq2_job | pass | {"details": {"job_id": "bbd44e69cb8906b564432cfe370df579", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy2"}} |
| result_table | pass | {"details": {"data_type": "galaxy.datatypes.tabular.Tabular", "extension": "tabular", "file_size": 4889011, "genome_build": "?", "history_content_type": "dataset", "id": "f9cad7b01a4721351f790a52bb713318", "misc_blurb": "47,729 lines 7 columns", "name": "DESeq2 result file on dataset 9-17 and collection 18", "state": "ok", "visible": true}} |
| bioartifact_de_table_contract | pass | {"details": {"contract": "de_table", "validation_copy": "deseq2_results.de_table_contract.tsv"}} |
| raw_de_table_contract | warning | {"details": {"passed": false, "raw_result": "deseq2_results.tsv", "reason": "Galaxy DESeq2 download has no header and includes rows with missing p-values; a normalized finite-row copy was used for the strict contract."}} |