WDL-bench

Bioinformatics agent benchmark from WDL workflow pipelines (WARP, ENCODE, BioWDL).

Derived from three major WDL workflow sources:

• WARP (Broad Institute): 15 production genomics pipelines with Verify WDLs
• ENCODE-DCC: 8 consortium-standard epigenomics/transcriptomics pipelines
• BioWDL (Leiden UMC): 15 modular pipelines with pytest-workflow tests
• Broad viral-pipelines: 5 viral genomics workflows with expected output JSONs

Companion to IWC-bench (75 Galaxy tasks), GTN-bench (53 Galaxy tasks), and nf-core-bench (69 Nextflow tasks).

Tasks (43 total)

Sources: BioWDL (15), WARP (15), ENCODE (8), Broad-viral (5).

Difficulty distribution: 3 easy, 16 medium, 23 hard, 1 expert — sorted by difficulty below.

#	Task ID	Source	Difficulty	Domain	Assertions
1	chip_seq	BioWDL	easy	epigenetics	4
2	gatk_preprocess	BioWDL	easy	preprocessing	9
3	structural_variantcalling	BioWDL	easy	variant-calling	20
4	aligning	BioWDL	medium	alignment	8
5	bam_metrics	BioWDL	medium	quality-control	70
6	bam_to_gvcf	BioWDL	medium	variant-calling	3
7	expression_quantification	BioWDL	medium	transcriptomics	32
8	gatk_variantcalling	BioWDL	medium	variant-calling	51
9	jointgenotyping	BioWDL	medium	variant-calling	12
10	pacbio_variantcalling	BioWDL	medium	variant-calling	45
11	qc	BioWDL	medium	quality-control	91
12	small_rna	BioWDL	medium	transcriptomics	36
13	arrays	WARP	medium	genomics	12
14	build_indices	WARP	medium	genomics	1
15	dna_seq	WARP	medium	genomics	5
16	paired_tag	WARP	medium	genomics	12
17	peak_calling	WARP	medium	genomics	1
18	rna_seq_warp	WARP	medium	genomics	14
19	smartseq2_single_nucleus_multisample	WARP	medium	genomics	2
20	germline_dna	BioWDL	hard	variant-calling	261
21	rna_seq	BioWDL	hard	transcriptomics	120
22	viral_assemble_denovo	Broad-viral	hard	virology	10
23	viral_assemble_refbased	Broad-viral	hard	virology	15
24	viral_load_illumina_fastqs	Broad-viral	hard	virology	2
25	viral_load_illumina_fastqs_deplete	Broad-viral	hard	virology	2
26	viral_sarscov2_lineages	Broad-viral	hard	virology	4
27	atac_seq	ENCODE	hard	epigenetics	24
28	chip_seq_encode	ENCODE	hard	epigenetics	24
29	dnase_seq	ENCODE	hard	epigenetics	125
30	hi_c	ENCODE	hard	3d-genome	43
31	long_read_rna_seq	ENCODE	hard	transcriptomics	19
32	mirna_seq	ENCODE	hard	transcriptomics	3
33	rna_seq_encode	ENCODE	hard	transcriptomics	6
34	wgbs	ENCODE	hard	epigenetics	18
35	atac	WARP	hard	genomics	7
36	genotyping	WARP	hard	genomics	5
37	multiome	WARP	hard	genomics	12
38	optimus	WARP	hard	genomics	7
39	reprocessing	WARP	hard	genomics	1
40	slideseq	WARP	hard	genomics	6
41	slidetags	WARP	hard	genomics	12
42	snm3c	WARP	hard	genomics	3
43	somatic_variantcalling	BioWDL	expert	variant-calling	308

Quick start

git clone https://github.com/lingzhi227/WDL-bench.git
cd WDL-bench
python3 src/dataset.py list-tasks -v

Task format

tasks/{task-id}/
  prompt_open.md          # Biological question
  prompt_guided.md        # Pipeline invocation
  rubric.json             # Ground truth and scoring
  wdl/                    # WDL workflow files
  tests/                  # Test configs and data (BioWDL)

Citation

@article{voss2017full,
  title={Full-stack genomics pipelining with GATK4+ WDL+ Cromwell},
  author={Voss, Kate and Van der Auwera, Geraldine and Gentry, Jeff},
  year={2017}
}