Bioinformatics-Workflow-Bench

142 execution-verified bioinformatics workflow tasks across Galaxy, Nextflow, and WDL platforms.

Overview

Bioinformatics-Workflow-Bench is a unified benchmark for evaluating AI agents on real-world bioinformatics workflow execution tasks. It merges 142 execution-verified tasks from four peer-reviewed sources:

Source	Platform	Tasks	Ground Truth	Verification Method
IWC	Galaxy	75	Planemo test assertions	CI-verified on every PR
nf-core	Nextflow	45	nf-test MD5 snapshots	Docker execution + snapshot comparison
GTN	Galaxy	14	Planemo test assertions	Execution on usegalaxy.org
BioWDL / WARP / ENCODE	WDL	8	pytest-workflow	miniwdl + Docker execution

Difficulty distribution: 31 easy, 52 medium, 37 hard, 22 expert.

Every task has been executed end-to-end and its outputs verified against ground truth assertions filed by human domain experts. No task is included based on structural validation alone.

What makes this benchmark different?

• Execution-verified ground truth: Every task has been run on a real compute platform with outputs checked against expert-filed assertions
• Three workflow platforms: Galaxy (.ga), Nextflow (nf-core), and WDL -- tests agent adaptability across ecosystems
• Peer-reviewed workflows: All source workflows passed human code review and automated CI before publication
• Real experimental data: Input data from Zenodo DOIs, nf-core test profiles, or bundled test datasets -- no simulated data
• Three prompt tiers: Each task has open (biological question only), guided (tool names given), and assisted (step-by-step scaffold) prompts
• Task-specific rubrics: Auto-generated evaluation rubrics with expected steps, output assertions, and scoring weights
• Wide domain coverage: 35 domains from genomics to computational chemistry, single-cell to metagenomics

Tasks

Galaxy / IWC (75 tasks)

#	Task ID	Name	Difficulty	Domain	Steps	Assertions	Notes
1	iwc--velocyto	Velocyto	easy	scRNAseq	1	1	IWC Planemo CI verified
2	iwc--avg-bigwig	Avg Bigwig	easy	other	2	2	IWC Planemo CI verified
3	iwc--baredsc	Baredsc	easy	scRNAseq	2	23	IWC Planemo CI verified
4	iwc--short-read-qc	Short Read Qc	easy	read-preprocessing	2	2	IWC Planemo CI verified
5	iwc--cgmlst-bacterial-genome	Cgmlst Bacterial Genome	easy	bacterial_genomics	3	7	IWC Planemo CI verified
6	iwc--assembly-with-flye	Assembly With Flye	easy	genome-assembly	4	10	IWC Planemo CI verified
7	iwc--fastq-to-matrix-10x	Fastq To Matrix 10X	easy	scRNAseq	4	5	IWC Planemo CI verified
8	iwc--hyphy	Hyphy	easy	comparative_genomics	4	8	IWC Planemo CI verified
9	iwc--parallel-accession-download	Parallel Accession Download	easy	data-fetching	4	1	IWC Planemo CI verified
10	iwc--qcxms-sdf	Qcxms Sdf	easy	metabolomics	4	1	IWC Planemo CI verified
11	iwc--bacterial-genome-assembly	Bacterial Genome Assembly	easy	genome-assembly	5	6	IWC Planemo CI verified
12	iwc--brew3r	Brew3R	easy	transcriptomics	5	2	IWC Planemo CI verified
13	iwc--goseq	Goseq	easy	transcriptomics	5	25	IWC Planemo CI verified
14	iwc--lncrna-annotation	Lncrna Annotation	easy	genome_annotation	5	10	IWC Planemo CI verified
15	iwc--vgp0-mitogenome	Vgp0 Mitogenome	easy	VGP-assembly	5	4	IWC Planemo CI verified
16	iwc--annotation-braker3	Annotation Braker3	medium	genome_annotation	6	12	IWC Planemo CI verified
17	iwc--amr-gene-detection	Amr Gene Detection	medium	other	7	21	IWC Planemo CI verified
18	iwc--annotation-helixer	Annotation Helixer	medium	genome_annotation	7	13	IWC Planemo CI verified
19	iwc--chipseq-pe	Chipseq Pe	medium	epigenetics	7	18	IWC Planemo CI verified
20	iwc--chipseq-sr	Chipseq Sr	medium	epigenetics	7	18	IWC Planemo CI verified
21	iwc--gcms-metams	Gcms Metams	medium	metabolomics	7	7	IWC Planemo CI verified
22	iwc--nuclei-segmentation	Nuclei Segmentation	medium	imaging	7	3	IWC Planemo CI verified
23	iwc--raw-reads-qc	Raw Reads Qc	medium	other	7	10	IWC Planemo CI verified
24	iwc--annotation-maker	Annotation Maker	medium	genome_annotation	8	19	IWC Planemo CI verified
25	iwc--openms-metaprosip	Openms Metaprosip	medium	proteomics	8	6	IWC Planemo CI verified
26	iwc--polish-long-reads	Polish Long Reads	medium	other	8	1	IWC Planemo CI verified
27	iwc--bacterial-genome-annotation	Bacterial Genome Annotation	medium	bacterial_genomics	9	15	IWC Planemo CI verified
28	iwc--cutandrun	Cutandrun	medium	epigenetics	9	17	IWC Planemo CI verified
29	iwc--mfassignr	Mfassignr	medium	metabolomics	9	15	IWC Planemo CI verified
30	iwc--protein-ligand-param	Protein Ligand Param	medium	other	9	2	IWC Planemo CI verified
31	iwc--sars-cov2-se-wgs	Sars Cov2 Se Wgs	medium	sars-cov-2-variant-calling	9	2	IWC Planemo CI verified
32	iwc--mag-genome-annotation-parallel	Mag Genome Annotation Parallel	medium	microbiome	10	7	IWC Planemo CI verified
33	iwc--fragment-docking	Fragment Docking	medium	computational-chemistry	11	1	IWC Planemo CI verified
34	iwc--rnaseq-sr	Rnaseq Sr	medium	transcriptomics	11	9	IWC Planemo CI verified
35	iwc--sars-cov2-pe-wgs	Sars Cov2 Pe Wgs	medium	sars-cov-2-variant-calling	11	1	IWC Planemo CI verified
36	iwc--vgp2-kmer-trio	Vgp2 Kmer Trio	medium	VGP-assembly	11	7	IWC Planemo CI verified
37	iwc--vgp9-decontamination	Vgp9 Decontamination	medium	VGP-assembly	11	18	IWC Planemo CI verified
38	iwc--generic-vc	Generic Vc	medium	other	12	5	IWC Planemo CI verified
39	iwc--lcms-preprocessing	Lcms Preprocessing	medium	metabolomics	12	2	IWC Planemo CI verified
40	iwc--ploidy-vc	Ploidy Vc	medium	other	12	8	IWC Planemo CI verified
41	iwc--rnaseq-pe	Rnaseq Pe	medium	transcriptomics	12	11	IWC Planemo CI verified
42	iwc--vgp7-scaffolding-bionano	Vgp7 Scaffolding Bionano	medium	VGP-assembly	12	5	IWC Planemo CI verified
43	iwc--bacterial-qc-post-assembly	Bacterial Qc Post Assembly	medium	bacterial_genomics	13	18	IWC Planemo CI verified
44	iwc--haploid-vc	Haploid Vc	medium	other	13	4	IWC Planemo CI verified
45	iwc--pseudobulk-decoupler-edger	Pseudobulk Decoupler Edger	medium	other	13	5	IWC Planemo CI verified
46	iwc--sra-manifest-fastqs	Sra Manifest Fastqs	medium	other	13	2	IWC Planemo CI verified
47	iwc--dada2	Dada2	medium	amplicon	14	9	IWC Planemo CI verified
48	iwc--vgp-plot-nx-size	Vgp Plot Nx Size	medium	VGP-assembly	14	4	IWC Planemo CI verified
49	iwc--vgp1-kmer-profiling	Vgp1 Kmer Profiling	medium	VGP-assembly	14	9	IWC Planemo CI verified
50	iwc--gromacs-mmgbsa	Gromacs Mmgbsa	hard	computational-chemistry	17	4	IWC Planemo CI verified
51	iwc--rnaseq-de	Rnaseq De	hard	transcriptomics	17	6	IWC Planemo CI verified
52	iwc--sars-cov2-consensus	Sars Cov2 Consensus	hard	sars-cov-2-variant-calling	17	1	IWC Planemo CI verified
53	iwc--metagenomic-raw-reads-amr	Metagenomic Raw Reads Amr	hard	microbiome	20	22	IWC Planemo CI verified
54	iwc--sars-cov2-ivar	Sars Cov2 Ivar	hard	sars-cov-2-variant-calling	20	5	IWC Planemo CI verified
55	iwc--gromacs-dctmd	Gromacs Dctmd	hard	computational-chemistry	21	6	IWC Planemo CI verified
56	iwc--consensus-peaks	Consensus Peaks	hard	epigenetics	22	7	IWC Planemo CI verified
57	iwc--mags-taxonomy-annotation	Mags Taxonomy Annotation	hard	microbiome	22	14	IWC Planemo CI verified
58	iwc--sars-cov2-ont-artic	Sars Cov2 Ont Artic	hard	sars-cov-2-variant-calling	22	1	IWC Planemo CI verified
59	iwc--viral-generic	Viral Generic	hard	other	23	13	IWC Planemo CI verified
60	iwc--sars-cov2-pe-artic	Sars Cov2 Pe Artic	hard	sars-cov-2-variant-calling	25	2	IWC Planemo CI verified
61	iwc--atacseq	Atacseq	hard	epigenetics	27	19	IWC Planemo CI verified
62	iwc--sars-cov2-reporting	Sars Cov2 Reporting	hard	sars-cov-2-variant-calling	30	2	IWC Planemo CI verified
63	iwc--variation-reporting	Variation Reporting	hard	sars-cov-2-variant-calling	31	4	IWC Planemo CI verified
64	iwc--metagenomic-genes-catalogue	Metagenomic Genes Catalogue	hard	microbiome	33	17	IWC Planemo CI verified
65	iwc--vgp6b-purge-dups-haplotype	Vgp6B Purge Dups Haplotype	hard	VGP-assembly	35	10	IWC Planemo CI verified
66	iwc--mags-building	Mags Building	expert	microbiome	38	5	IWC Planemo CI verified
67	iwc--vgp3-hifi-assembly	Vgp3 Hifi Assembly	expert	VGP-assembly	42	11	IWC Planemo CI verified
68	iwc--vgp5-hifi-trio-assembly	Vgp5 Hifi Trio Assembly	expert	VGP-assembly	44	8	IWC Planemo CI verified
69	iwc--vgp6-purge-dups	Vgp6 Purge Dups	expert	VGP-assembly	45	13	IWC Planemo CI verified
70	iwc--binning-evaluation	Binning Evaluation	expert	microbiome	47	7	IWC Planemo CI verified
71	iwc--influenza	Influenza	expert	virology	54	8	IWC Planemo CI verified
72	iwc--scanpy-clustering	Scanpy Clustering	expert	scRNAseq	55	51	IWC Planemo CI verified
73	iwc--vgp8-scaffolding-hic	Vgp8 Scaffolding Hic	expert	VGP-assembly	55	17	IWC Planemo CI verified
74	iwc--hic-contact-map	Hic Contact Map	expert	VGP-assembly	56	22	IWC Planemo CI verified
75	iwc--vgp4-hifi-hic-assembly	Vgp4 Hifi Hic Assembly	expert	VGP-assembly	57	22	IWC Planemo CI verified

Galaxy / GTN (14 tasks)

#	Task ID	Name	Difficulty	Domain	Steps	Assertions	Notes
1	gtn--abc_intro_phylo	Abc Intro Phylo	easy	evolution	3	3	Verified with planemo test on usegalaxy.org. All assertions passed.
2	gtn--bacterial-isolate-species-contamination-checking	Bacterial Isolate Species Contamination Checking	easy	ecology	3	5	Verified on usegalaxy.org
3	gtn--mitochondrion-assembly	Mitochondrion Assembly	easy	assembly	3	4	Verified on usegalaxy.org
4	gtn--quality-contamination-control	Quality Contamination Control	easy	sequence-analysis	5	6	Verified on usegalaxy.org
5	gtn--small_ncrna_clustering	Small Ncrna Clustering	easy	transcriptomics	5	4	Verified on usegalaxy.org
6	gtn--mrsa-illumina	Mrsa Illumina	medium	assembly	6	4	Verified on usegalaxy.org
7	gtn--unicycler-assembly	Unicycler Assembly	medium	assembly	6	3	Verified on usegalaxy.org
8	gtn--med-chem-data	Med Chem Data	medium	comp-chem	7	8	Verified on usegalaxy.org
9	gtn--scrna-raceid	Scrna Raceid	medium	scRNAseq	8	3	Verified interactively on usegalaxy.org. All 23 jobs completed. Trajectory analy
10	gtn--galaxy-intro-101-everyone	Galaxy Intro 101 Everyone	medium	introductory	9	4	Verified on usegalaxy.org
11	gtn--assembly-decontamination	Assembly Decontamination	medium	assembly	10	3	Verified with planemo test on usegalaxy.org. All assertions passed.
12	gtn--hybrid_denovo_assembly	Hybrid Denovo Assembly	medium	assembly	12	11	Verified on usegalaxy.org
13	gtn--gtn-hic-drosophila	Gtn Hic Drosophila	hard	epigenetics	18	2	Verified on usegalaxy.org
14	gtn--tal1-binding-site-identification	Tal1 Binding Site Identification	expert	epigenetics	57	3	Verified on usegalaxy.org

Nextflow / nf-core (45 tasks)

#	Task ID	Name	Difficulty	Domain	Steps	Assertions	Notes
1	nfcore--metaboigniter	nf-core/metaboigniter	easy	metagenomics	2	3	Verified with nf-test snapshots
2	nfcore--ribomsqc	nf-core/ribomsqc	easy	other	2	14	Verified with nf-test snapshots
3	nfcore--drugresponseeval	nf-core/drugresponseeval	easy	other	3	10	Verified with nf-test snapshots
4	nfcore--nanostring	nf-core/nanostring	easy	gene-expression	3	13	Verified on Docker workstation. Pipeline completed successfully.
5	nfcore--fetchngs	nf-core/fetchngs	easy	metagenomics	4	55	27/30 strict MD5 match. 2 'missing' are pipeline_info files with timestamps in f
6	nfcore--epitopeprediction	nf-core/epitopeprediction	easy	other	5	139	Verified with nf-test snapshots
7	nfcore--detaxizer	nf-core/detaxizer	medium	other	8	46	Verified with nf-test snapshots
8	nfcore--fastqrepair	nf-core/fastqrepair	medium	other	8	39	15/30 strict MD5 match. All 15 mismatches are MultiQC report files (SVG plots, l
9	nfcore--molkart	nf-core/molkart	medium	other	8	18	Verified on Docker workstation. Pipeline completed successfully.
10	nfcore--airrflow	nf-core/airrflow	medium	other	9	51	Docker-only pipeline. 18/18 snapshot MD5s matched on Docker profile.
11	nfcore--readsimulator	nf-core/readsimulator	medium	simulation	9	8	Verified with nf-test snapshots
12	nfcore--hic	nf-core/hic	medium	3d-genome	10	18	Verified on Docker workstation. Pipeline completed successfully.
13	nfcore--bamtofastq	nf-core/bamtofastq	medium	other	12	34	Verified with nf-test snapshots
14	nfcore--pairgenomealign	nf-core/pairgenomealign	medium	sequence-analysis	12	20	Verified on Docker workstation. Pipeline completed successfully.
15	nfcore--mhcquant	nf-core/mhcquant	medium	proteomics	13	107	Verified with nf-test snapshots
16	nfcore--isoseq	nf-core/isoseq	medium	transcriptomics	14	148	20/30 strict MD5 match. 15 expected files are BAM/PBI excluded from MD5 computat
17	nfcore--phyloplace	nf-core/phyloplace	medium	other	15	31	Verified with nf-test snapshots
18	nfcore--coproid	nf-core/coproid	hard	other	16	1	Verified on Docker workstation. Pipeline completed successfully.
19	nfcore--pangenome	nf-core/pangenome	hard	pangenomics	16	39	Verified with nf-test snapshots
20	nfcore--demultiplex	nf-core/demultiplex	hard	data-processing	17	301	Verified on Docker workstation. Pipeline completed successfully.
21	nfcore--differentialabundance	nf-core/differentialabundance	hard	other	19	53	Conda GUNZIP path unresolvable. Docker profile works. Verified on Docker worksta
22	nfcore--createtaxdb	nf-core/createtaxdb	hard	metagenomics	20	21	Verified on Docker workstation. Pipeline completed successfully.
23	nfcore--scrnaseq	nf-core/scrnaseq	hard	transcriptomics	20	136	Docker-only pipeline (CELLRANGERARC_COUNT requires Docker). Verified on Docker w
24	nfcore--magmap	nf-core/magmap	hard	metagenomics	21	80	Verified with nf-test snapshots
25	nfcore--pacvar	nf-core/pacvar	hard	variant-calling	21	12	Verified with nf-test snapshots
26	nfcore--genomeassembler	nf-core/genomeassembler	hard	assembly	22	33	7/8 strict MD5 match. 1 mismatch is assembler output (Flye/Hifiasm non-determini
27	nfcore--methylong	nf-core/methylong	hard	epigenetics	23	38	Verified with nf-test snapshots
28	nfcore--metatdenovo	nf-core/metatdenovo	hard	metagenomics	24	5	0/5 strict MD5 match. All 5 expected entries are 'versions.yml' from different m
29	nfcore--scnanoseq	nf-core/scnanoseq	hard	scRNAseq	25	2	Verified with nf-test snapshots
30	nfcore--smrnaseq	nf-core/smrnaseq	hard	transcriptomics	30	156	Verified on Docker workstation. Pipeline completed successfully.
31	nfcore--multiplesequencealign	nf-core/multiplesequencealign	hard	sequence-analysis	31	16	Verified with nf-test snapshots
32	nfcore--atacseq	nf-core/atacseq	hard	epigenetics	34	189	Verified on Docker workstation. Pipeline completed successfully. (Failed on cond
33	nfcore--chipseq	nf-core/chipseq	hard	epigenetics	34	397	Verified with nf-test snapshots
34	nfcore--callingcards	nf-core/callingcards	hard	other	35	370	25/30 strict MD5 match. 5 mismatches are biologically equivalent: genes.bed (ref
35	nfcore--variantbenchmarking	nf-core/variantbenchmarking	expert	variant-calling	36	52	Verified on Docker workstation. Pipeline completed successfully.
36	nfcore--pathogensurveillance	nf-core/pathogensurveillance	expert	other	37	73	Verified with nf-test snapshots
37	nfcore--methylseq	nf-core/methylseq	expert	epigenetics	39	134	Verified with nf-test snapshots
38	nfcore--phaseimpute	nf-core/phaseimpute	expert	other	39	13	0/12 on conda (all MD5 mismatch). Docker profile produces correct outputs. Verif
39	nfcore--riboseq	nf-core/riboseq	expert	other	40	231	Verified on Docker workstation. Pipeline completed successfully.
40	nfcore--rnavar	nf-core/rnavar	expert	transcriptomics	41	27	21/25 strict MD5 match. 2 'missing' are BAM files excluded from MD5 by design (.
41	nfcore--nascent	nf-core/nascent	expert	other	51	67	23/30 strict MD5 match. 7 mismatches are biologically equivalent: 6 samtools sta
42	nfcore--taxprofiler	nf-core/taxprofiler	expert	metagenomics	53	7	7/7 strict MD5 match (100%). Pipeline exit=1 from a non-essential late step. All
43	nfcore--viralrecon	nf-core/viralrecon	expert	variant-calling	57	158	Verified on Docker workstation. Pipeline completed successfully.
44	nfcore--viralmetagenome	nf-core/viralmetagenome	expert	variant-calling	69	258	22/30 strict MD5 match. 8 mismatches are biologically equivalent: all are assemb
45	nfcore--rnaseq	nf-core/rnaseq	expert	transcriptomics	70	657	Verified with nf-test snapshots

WDL (8 tasks)

#	Task ID	Name	Difficulty	Domain	Steps	Assertions	Notes
1	wdl--qc	Qc	easy	quality-control	2	91	Verified with miniwdl + Docker. Pipeline completed successfully.
2	wdl--aligning	Aligning	easy	alignment	4	8	Verified with miniwdl + Docker. Pipeline completed successfully.
3	wdl--expression_quantification	Expression Quantification	easy	transcriptomics	4	32	Verified with miniwdl + Docker.
4	wdl--bam_metrics	Bam Metrics	easy	quality-control	5	70	Verified with miniwdl + Docker. Pipeline completed successfully.
5	wdl--gatk_preprocess	Gatk Preprocess	easy	preprocessing	5	9	Verified with miniwdl + Docker. Pipeline completed successfully.
6	wdl--gatk_variantcalling	Gatk Variantcalling	hard	variant-calling	17	51	Verified with miniwdl + Docker. Pipeline completed successfully (exit 0).
7	wdl--structural_variantcalling	Structural Variantcalling	hard	variant-calling	23	20	Verified with miniwdl + Docker. Pipeline completed successfully.
8	wdl--somatic_variantcalling	Somatic Variantcalling	hard	variant-calling	25	308	Verified with miniwdl + Docker. Pipeline completed successfully (exit 0).

# Clone
git clone https://github.com/lingzhi227/Bioinformatics-Workflow-Bench.git
cd Bioinformatics-Workflow-Bench

# List all tasks
python src/dataset.py list-tasks

# Filter by platform or difficulty
python src/dataset.py list-tasks --platform galaxy
python src/dataset.py list-tasks --difficulty hard

# Show task details
python src/dataset.py show-task --task iwc--rnaseq-pe

# Show ground truth assertions
python src/dataset.py show-assertions --task nfcore--rnaseq

# Download input data
python src/dataset.py download --task gtn--mrsa-illumina

Task format

tasks/{source}--{task-id}/
  prompt_open.md              # Biological question only (agent must infer tools and pipeline)
  prompt_guided.md            # Pipeline structure with tool names
  prompt_assisted.md          # Step-by-step scaffold with verification hints
  rubric.json                 # Evaluation rubric (steps, assertions, scoring weights)

  # Platform-specific files:
  # Galaxy (IWC/GTN):
  workflow/
    *.ga                      # Galaxy workflow file
    *-tests.yml               # Planemo test assertions (ground truth)
    test-data/                # Local test data (if any)
  environment.yml             # Conda environment
  Dockerfile                  # Container definition
  run_script.sh               # Execution script (IWC only)

  # Nextflow (nf-core):
  nfcore/
    test.config               # Nextflow test configuration
    nextflow_schema.json       # Parameter schema
    tests/*.nf.test           # nf-test definitions
    tests/*.nf.test.snap      # Snapshot assertions (MD5 ground truth)
  test_config.txt             # Original test config

  # WDL:
  wdl/
    *.wdl                     # WDL workflow files
  tests/
    *.json                    # Input JSONs
    data/                     # Test data

Prompt tiers

• prompt_open.md: Describes only the biological objective. The agent must determine which tools, pipeline, and parameters to use. Tests biological reasoning + autonomous planning.
• prompt_guided.md: Provides the pipeline structure with tool names. Tests whether the agent can execute a known workflow correctly.
• prompt_assisted.md: Adds explicit step ordering and verification targets. Tests reproducibility with reduced planning ambiguity.

The delta across open/guided/assisted scores reveals where agents struggle: biological reasoning, tool selection, or faithful execution.

rubric.json schema

{
  "task_id": "iwc--rnaseq-pe",
  "original_task_id": "rnaseq-pe",
  "platform": "galaxy",
  "source": "IWC",
  "verification": "execution-verified",
  "metadata": {
    "difficulty": "medium",
    "domain": "transcriptomics",
    "biological_steps": 6,
    "assertion_count": 24,
    "primary_tools": ["hisat2", "featurecounts", "deseq2"]
  },
  "scoring_weights": {
    "pipeline_completion": 0.4,
    "result_correctness": 0.4,
    "biological_validity": 0.2
  }
}

Evaluation

# Deterministic rubric-based evaluation
python scripts/eval_agent.py --task iwc--rnaseq-pe --workspace /path/to/agent/output

# Agentic LLM judge (requires OpenAI API key)
python scripts/judge_agent.py --task nfcore--rnaseq --workspace /path/to/output \
  --api-key "$OPENAI_API_KEY"

Scoring formula: 40% pipeline completion + 40% result correctness + 20% biological validity.

Domain coverage

Domain	Tasks	Platforms
other	27	galaxy, nextflow
VGP-assembly	13	galaxy
transcriptomics	12	galaxy, nextflow, wdl
epigenetics	11	galaxy, nextflow
sars-cov-2-variant-calling	8	galaxy
variant-calling	7	nextflow, wdl
scRNAseq	6	galaxy, nextflow
microbiome	6	galaxy
metagenomics	6	nextflow
assembly	6	galaxy, nextflow
genome_annotation	4	galaxy
metabolomics	4	galaxy
bacterial_genomics	3	galaxy
computational-chemistry	3	galaxy
sequence-analysis	3	galaxy, nextflow
genome-assembly	2	galaxy
proteomics	2	galaxy, nextflow
quality-control	2	wdl
amplicon	1	galaxy
comparative_genomics	1	galaxy

Provenance

This benchmark merges execution-verified tasks from four independently maintained repositories:

• IWC-bench (75 tasks): Galaxy Intergalactic Workflow Commission workflows with Planemo CI
• nf-core-bench (45 tasks): nf-core Nextflow pipelines with nf-test snapshot verification
• GTN-bench (14 tasks): Galaxy Training Network tutorial workflows verified on usegalaxy.org
• WDL-bench (8 tasks): BioWDL/WARP/ENCODE WDL pipelines verified with miniwdl

Each task directory preserves all original files from its source repository. The rubric.json contains original_task_id and source fields for full traceability.

Citation

@article{hiltemann2023galaxy,
  title={Galaxy Training: A powerful framework for teaching!},
  author={Hiltemann, Saskia and others},
  journal={PLoS Computational Biology},
  volume={19},
  pages={e1010752},
  year={2023}
}

@article{ewels2020nf,
  title={The nf-core framework for community-curated bioinformatics pipelines},
  author={Ewels, Philip A and others},
  journal={Nature Biotechnology},
  volume={38},
  pages={276--278},
  year={2020}
}