IWC benchmark item

wf_006_atacseq_chromatin_accessibility

ATAC-seq Analysis: Chromatin Accessibility Profiling

ATAC-seq Chromatin Accessibility Profiling

Open source IWC workflowGround-truth Galaxy history

Reference workflow

27 tool steps across 21 unique tools, including tools inside nested subworkflows. A plus sign denotes parallel branches.

Workflow
Fastp (remove adapter and bad quality reads)Bowtie2 map on referencefilter MAPQ30 concordant pairs and not mitochondrial pairs + Get number of reads per chromosomeremove PCR duplicates + reads in chrM/MT for multiQCconvert BAM to BED to improve peak calling + Compute fragment length histogram + number of readsCall Peak with MACS2 + remove comments lines + compute 1/million readsBigwig from MACS2 (no norm) + summary of MACS2 + get summits +/-500kb + Convert 1/million reads to parameterIsolate each bigwig do normalize not average + Merge summits +/-500kbnormalize by million reads + Compute coverage on summits +/-500kbnumber of reads in peakscompute 1/million reads in peaks + Combine number of reads in peaks with total number of readsConvert 1/million reads in peaks to parameter + reads in peaks multiQCnormalize by million reads in peaks + MultiQC

Complete query

The full task shown to the agent, excluding execution-condition instructions.

Identify open-chromatin regions in the provided paired-end human ATAC-seq sample using the hg19 assembly.
Remove Nextera adapters by mate-overlap analysis. Treat bases below Phred 20 as low quality, and discard a pair if either mate contains more than 70 percent low-quality bases or is shorter than 15 bases after adapter trimming.
Align the surviving pairs to hg19 with a suitable paired-end short-read aligner. Retain pairs that the selected aligner classifies as valid paired-end alignments, with mapping quality at least 30, remove mitochondrial alignments, and remove PCR duplicates.
Call open-chromatin regions on the resulting alignments with a peak caller suitable for ATAC-seq, using a q-value cutoff of 0.05 and no control sample.
Write the results to `final_answer/peaks.bed`, with chromosome, start, and end in the first three tab-separated columns. Report one BED record for every interval your peak caller reports, even when several records share the same chromosome, start, and end coordinates. Do not deduplicate those records.
Write `final_answer/method.json` as a JSON object with the keys `aligner` and `peak_caller`, whose values are the common names of the aligner and the peak caller you used.

acc evaluator

acc compares the final output files with the reference outputs.

Metric
interval_f1
Definition

Precision/recall F1 over peaks matched by reciprocal overlap. A candidate peak and a reference peak count as the same region when each covers at least the required fraction of the other, so a call that is shifted or much wider than the reference does not match. Matching is one-to-one, so splitting one reference peak into several candidate peaks cannot be rewarded more than once.

Formula
Final scoreS = F1(M, N_C, N_R)

M is the maximum number of one-to-one candidate/reference peak matches.

Reciprocal overlapq(c,r) = min(O/|c|, O/|r|); O = max(0, min(end_c,end_r) − max(start_c,start_r))

Candidate and reference peaks must be on the same chromosome.

Match rulec ↔ r only if q(c,r) ≥ 0.5

Maximum bipartite matching prevents split peaks from matching one reference peak more than once.

Step-score requirements

A step passes when the trace directly shows that it ran. Parameter correctness and output quality are measured separately by acc.

  1. Step 1Remove Nextera adapters and apply the stated Q20, 70%-low-quality-base, and 15-base filters.
    • A successful paired-read trimming execution removed/detected Nextera adapters.
    • The successful execution used Q20, at most 70% low-quality bases, and minimum length 15.
    • The resulting paired reads were consumed by the alignment chain.
  2. Step 2Align the surviving pairs to hg19 using a suitable paired-end short-read aligner.
    • A successful paired-end short-read alignment used hg19, not hg38 or another assembly.
    • The aligned output derives from the step-1 surviving pairs.
  3. Step 3Retain valid paired-end alignments with mapping quality at least 30 and remove mitochondrial alignments.
    • The retained alignments satisfy the aligner's valid/proper paired-end criterion.
    • The retained alignments have mapping quality at least 30.
    • Mitochondrial alignments were excluded before duplicate removal and peak calling.
  4. Step 4Remove PCR duplicates.
    • PCR duplicates were identified and removed from the filtered nuclear paired alignments.
    • Peak calling consumed the duplicate-removed alignments.
  5. Step 5Call open-chromatin regions using an ATAC-seq-suitable peak caller with q-value ≤ 0.05 and no control, preserving one BED row per reported interval.
    • An ATAC-seq-suitable peak caller ran successfully on the step-4 alignments with no control and q-value threshold at most 0.05.
    • The final BED preserves exactly one row per reported peak interval rather than expanding intervals base by base.
    • The required BED artifact passes schema and final-answer checks.

Model results and score explanations

The 13 results below acc 1.000 each include a score explanation and quantitative evidence. A score below 1.000 is not automatically an error. Each replicate shows its recorded workflow, acc, step score, and Hugging Face trace. Galaxy histories can be imported by link but are not published in Galaxy's public history listing.

GPT-5.5

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Reference downloadTrimming — fastpReference index — SAMtoolsAlignment name sort — SAMtoolsFixmate — SAMtoolsCoordinate sort — SAMtools4 more steps
All 10 recorded steps
  1. Reference download
  2. Trimming — fastp
  3. Reference index — SAMtools
  4. Alignment name sort — SAMtools
  5. Fixmate — SAMtools
  6. Coordinate sort — SAMtools
  7. Duplicate removal — SAMtools
  8. Final alignment filter — SAMtools + Filter rows
  9. Final deliverables — Table transformation
  10. Peak calling
Hugging Face trace
R2acc · step score 1.000
0.991
Recorded workflow
Tool setupReference downloadReference extractReference validation — Bowtie2Trim adapters and filter reads — fastpTool setup30 more steps
All 36 recorded steps
  1. Tool setup
  2. Reference download
  3. Reference extract
  4. Reference validation — Bowtie2
  5. Trim adapters and filter reads — fastp
  6. Tool setup
  7. Reference validation — Bowtie2
  8. Trim adapters and filter reads reuse — fastp
  9. Tool setup
  10. Reference validation — Bowtie2
  11. Trim adapters and filter reads reuse — fastp
  12. Tool setup
  13. Reference validation — Bowtie2
  14. Reference fasta reconstruction — Bowtie2
  15. Tool setup
  16. Reference validation — Bowtie2
  17. Tool setup
  18. Reference validation — Bowtie2
  19. Tool setup
  20. Reference validation — Bowtie2
  21. Tool setup
  22. Reference validation — Bowtie2
  23. Trim adapters and filter reads reuse — fastp
  24. Align to hg19 — Bowtie2 + SAMtools
  25. Tool setup
  26. Reference validation — Bowtie2
  27. Trim adapters and filter reads reuse — fastp
  28. Align to hg19 reuse — Bowtie2
  29. Name sort raw alignments — Bowtie2 + SAMtools
  30. Filter valid paired alignments mapq30 no mito — Bowtie2 + SAMtools + Filter rows
  31. Fixmate for duplicate marking — SAMtools
  32. Coordinate sort for duplicate marking — SAMtools
  33. Remove pcr duplicates — SAMtools
  34. Index deduplicated bam — SAMtools
  35. Call open chromatin regions
  36. Write final deliverables

Score explanation

Peak-boundary variation This Bowtie2 + MACS3 BED differs slightly from the method-specific target in peak boundaries and summit segmentation. Reciprocal-overlap matching penalizes those interval-level differences even when the accessible regions largely agree. Evidence. The complete interval set reached acc 0.991415; the residual is confined to peak representation.
Hugging Face trace
R3acc · step score 1.000
0.992
Recorded workflow
Trim reads — fastpSetup reference and tools — Bowtie2Align filter dedup — Bowtie2 + SAMtools + Filter rowsCall peaks and finalize — Table transformation
All 4 recorded steps
  1. Trim reads — fastp
  2. Setup reference and tools — Bowtie2
  3. Align filter dedup — Bowtie2 + SAMtools + Filter rows
  4. Call peaks and finalize — Table transformation

Score explanation

Peak-boundary variation This Bowtie2 + MACS3 BED differs slightly from the method-specific target in peak boundaries and summit segmentation. Reciprocal-overlap matching penalizes those interval-level differences even when the accessible regions largely agree. Evidence. The complete interval set reached acc 0.992498; the residual is confined to peak representation.
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
1.000
Recorded workflow
fastp ×2Bowtie2SAMtoolsPicard MarkDuplicatesMACS2
All 6 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. Picard MarkDuplicates
  6. MACS2
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp ×2Bowtie2Filter rows ×2Picard MarkDuplicatesBAMTools filterPicard MarkDuplicatesMACS2
All 9 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. Filter rows
  5. Filter rows
  6. Picard MarkDuplicates
  7. BAMTools filter
  8. Picard MarkDuplicates
  9. MACS2
Galaxy historyHugging Face trace
R3acc · step score 1.000
0.996
Recorded workflow
fastp ×2Bowtie2Data retrievalSAMtoolsPicard MarkDuplicatesSambamba SortGenrich ×2
All 9 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. Data retrieval
  5. SAMtools
  6. Picard MarkDuplicates
  7. Sambamba Sort
  8. Genrich
  9. Genrich

Score explanation

Peak-boundary variation This Bowtie2 + Genrich result differs slightly from the Genrich target in interval boundaries and count. The deficit reflects method-level peak representation rather than a missing output. Evidence. The complete interval set reached acc 0.995564 under one-to-one reciprocal-overlap matching.
Galaxy historyHugging Face trace

GPT-5.6 Sol

Open-ended code

R1acc · step score 1.000
0.923
Recorded workflow
Remove adapters and filter paired reads with fastpAlign surviving pairs to hg19 with Bowtie2Filter for valid MAPQ≥30 non-mitochondrial pairsRemove PCR duplicatesCall open-chromatin peaksExport and validate one BED row per peak
All 6 recorded steps
  1. Remove adapters and filter paired reads with fastp
  2. Align surviving pairs to hg19 with Bowtie2
  3. Filter for valid MAPQ≥30 non-mitochondrial pairs
  4. Remove PCR duplicates
  5. Call open-chromatin peaks
  6. Export and validate one BED row per peak

Score explanation

Extra summit splitting The MACS3 result split enriched regions into additional summit-centered records relative to the standard Bowtie2 + MACS3 target. Because matching is one-to-one, several submitted subpeaks cannot all match the same target interval. Evidence. The interval set reached acc 0.922735; the loss is concentrated in peak segmentation rather than a missing BED file.
Hugging Face trace
R2acc · step score 1.000
0.993
Recorded workflow
Tool setup localReference acquisitionReference index acquisitionAdapter quality filter — fastpBowtie2 reference index acquisitionPaired end alignment — Bowtie2 + SAMtools5 more steps
All 11 recorded steps
  1. Tool setup local
  2. Reference acquisition
  3. Reference index acquisition
  4. Adapter quality filter — fastp
  5. Bowtie2 reference index acquisition
  6. Paired end alignment — Bowtie2 + SAMtools
  7. Valid pair mapq mito filter — SAMtools + Filter rows + Table transformation
  8. Pcr duplicate removal — SAMtools
  9. Atac peak calling
  10. Successful branch selection
  11. Final export

Score explanation

Minor peak-boundary differences Bowtie2 and MACS3 produced almost the same peak set as the registered Bowtie2 + MACS3 result. A small number of intervals were added, omitted, or shifted enough to miss reciprocal-overlap matching. Evidence. The output reported 33,797 peaks versus 33,493; 33,420 matched. Precision was 0.988845 and recall was 0.997820.
Hugging Face trace
R3acc · step score 1.000
0.994
Recorded workflow
Remove adapters and filter paired reads with fastpAlign surviving pairs to hg19 with Bowtie2Filter for valid MAPQ≥30 non-mitochondrial pairsRemove PCR duplicatesCall open-chromatin peaksExport and validate one BED row per peak
All 6 recorded steps
  1. Remove adapters and filter paired reads with fastp
  2. Align surviving pairs to hg19 with Bowtie2
  3. Filter for valid MAPQ≥30 non-mitochondrial pairs
  4. Remove PCR duplicates
  5. Call open-chromatin peaks
  6. Export and validate one BED row per peak

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE no-model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 33,795 peaks versus 33,488; 33,449 matched. Precision was 0.989762 and recall was 0.998835.
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
0.996
Recorded workflow
fastp ×2Bowtie2Filter rows ×2Picard MarkDuplicatesMACS2
All 7 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. Filter rows
  5. Filter rows
  6. Picard MarkDuplicates
  7. MACS2

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE no-model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 33,462 peaks versus 33,488; 33,333 matched. Precision was 0.996145 and recall was 0.995371.
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp ×2Bowtie2SAMtoolsPicard MarkDuplicatesGenrich ×2Select columns
All 8 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. Picard MarkDuplicates
  6. Genrich
  7. Genrich
  8. Select columns
Galaxy historyHugging Face trace
R3acc · step score 1.000
0.995
Recorded workflow
fastp ×2Bowtie2Filter rows ×2Picard MarkDuplicatesMACS2
All 7 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. Filter rows
  5. Filter rows
  6. Picard MarkDuplicates
  7. MACS2

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE no-model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 33,535 peaks versus 33,488; 33,343 matched. Precision was 0.994275 and recall was 0.995670.
Galaxy historyHugging Face trace

GPT-5.6 Luna

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Input validationReference acquisitionAligner selectionAdapter trim and qc — fastpBwa reference indexBowtie2 reference index7 more steps
All 13 recorded steps
  1. Input validation
  2. Reference acquisition
  3. Aligner selection
  4. Adapter trim and qc — fastp
  5. Bwa reference index
  6. Bowtie2 reference index
  7. Aligner selection final — Bowtie2
  8. Alignment bowtie2 stream
  9. Pair level alignment filters — Filter rows
  10. Duplicate removal
  11. Peak calling
  12. Final bed projection
  13. Method metadata
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Remove adapters and filter paired reads with fastpAlign surviving pairs to hg19 with BWAFilter for valid MAPQ≥30 non-mitochondrial pairsRemove PCR duplicatesCall open-chromatin peaksExport and validate one BED row per peak
All 6 recorded steps
  1. Remove adapters and filter paired reads with fastp
  2. Align surviving pairs to hg19 with BWA
  3. Filter for valid MAPQ≥30 non-mitochondrial pairs
  4. Remove PCR duplicates
  5. Call open-chromatin peaks
  6. Export and validate one BED row per peak
Hugging Face trace
R3acc · step score 1.000
0.999507
Recorded workflow
Input inventoryReference preparation — SAMtoolsBowtie2 indexAdapter quality trim — fastp + Filter rowsPaired alignment — Bowtie2 + SAMtoolsPair filter matefix duplicate removal — SAMtools + Filter rows2 more steps
All 8 recorded steps
  1. Input inventory
  2. Reference preparation — SAMtools
  3. Bowtie2 index
  4. Adapter quality trim — fastp + Filter rows
  5. Paired alignment — Bowtie2 + SAMtools
  6. Pair filter matefix duplicate removal — SAMtools + Filter rows
  7. Peak call and bed export
  8. Deliverable validation — Table transformation

Score explanation

Minor peak-boundary differences Bowtie2 and MACS3 produced almost the same peak set as the registered Bowtie2 + MACS3 result. A small number of intervals were added, omitted, or shifted enough to miss reciprocal-overlap matching. Evidence. The output reported 33,504 peaks versus 33,493; 33,482 matched. Precision was 0.999343 and recall was 0.999672.
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
0.994
Recorded workflow
Data retrieval ×2fastp ×2Bowtie2SAMtoolsPicard MarkDuplicatesMACS22 more steps
All 89 recorded steps
  1. Data retrieval
  2. Data retrieval
  3. fastp
  4. fastp
  5. Bowtie2
  6. SAMtools
  7. Picard MarkDuplicates
  8. MACS2
  9. Select columns
  10. Table transformation
  11. Table transformation
  12. Table transformation
  13. Table transformation
  14. Table transformation
  15. Table transformation
  16. Table transformation
  17. Table transformation
  18. Table transformation
  19. Table transformation
  20. Table transformation
  21. Table transformation
  22. Table transformation
  23. Table transformation
  24. Table transformation
  25. Table transformation
  26. Table transformation
  27. Table transformation
  28. Table transformation
  29. Table transformation
  30. Table transformation
  31. Table transformation
  32. Table transformation
  33. Table transformation
  34. Table transformation
  35. Table transformation
  36. Table transformation
  37. Table transformation
  38. Table transformation
  39. Table transformation
  40. Table transformation
  41. Table transformation
  42. Table transformation
  43. Table transformation
  44. Table transformation
  45. Table transformation
  46. Table transformation
  47. Table transformation
  48. Table transformation
  49. Table transformation
  50. Table transformation
  51. Table transformation
  52. Table transformation
  53. Table transformation
  54. Table transformation
  55. Table transformation
  56. Table transformation
  57. Table transformation
  58. Table transformation
  59. Table transformation
  60. Table transformation
  61. Table transformation
  62. Table transformation
  63. Table transformation
  64. Table transformation
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  66. Table transformation
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  69. Table transformation
  70. Table transformation
  71. Table transformation
  72. Table transformation
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  74. Table transformation
  75. Table transformation
  76. Table transformation
  77. Table transformation
  78. Table transformation
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  80. Table transformation
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  85. Table transformation
  86. Table transformation
  87. Table transformation
  88. Table transformation
  89. Table transformation

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 38,549 peaks versus 38,779; 38,434 matched. Precision was 0.997017 and recall was 0.991103.
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp ×2Bowtie2SAMtools ×2Picard MarkDuplicatesMACS2
All 7 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. SAMtools
  6. Picard MarkDuplicates
  7. MACS2
Galaxy historyHugging Face trace
R3acc · step score 1.000
0.994
Recorded workflow
fastp ×2Bowtie2SAMtoolsPicard MarkDuplicatesMACS2
All 6 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. Picard MarkDuplicates
  6. MACS2

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 38,549 peaks versus 38,779; 38,434 matched. Precision was 0.997017 and recall was 0.991103.
Galaxy historyHugging Face trace

Codex + DeepSeek V4 Pro

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Reference hg19 downloadReference bowtie index acquisitionFastp adapter trimming and qcBowtie paired end alignment — SAMtoolsAlignment filter and coordinate sort — SAMtools + Filter rowsPcr duplicate removal — SAMtools + Filter rows2 more steps
All 8 recorded steps
  1. Reference hg19 download
  2. Reference bowtie index acquisition
  3. Fastp adapter trimming and qc
  4. Bowtie paired end alignment — SAMtools
  5. Alignment filter and coordinate sort — SAMtools + Filter rows
  6. Pcr duplicate removal — SAMtools + Filter rows
  7. Macs3 atac peak calling
  8. Final answer write
Hugging Face trace
R2acc · step score 1.000
0.990
Recorded workflow
Download hg19 referenceDownload prebuilt hg19 bwa indexTrim nextera adapters and quality filterAlign filtered reads — Bowtie2Filter alignments and remove duplicates — Filter rowsCall atac peaks
All 6 recorded steps
  1. Download hg19 reference
  2. Download prebuilt hg19 bwa index
  3. Trim nextera adapters and quality filter
  4. Align filtered reads — Bowtie2
  5. Filter alignments and remove duplicates — Filter rows
  6. Call atac peaks

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE no-model protocol. Its peak set is nearly identical to that protocol's reference, with small differences in interval boundaries and count. Evidence. The output reported 33,873 peaks versus 33,488; 33,349 matched. Precision was 0.984530 and recall was 0.995849.
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Remove adapters and filter paired reads with fastpAlign surviving pairs to hg19 with Bowtie2Align surviving pairs to hg19 with BWAFilter for valid MAPQ≥30 non-mitochondrial pairsRemove PCR duplicatesCall open-chromatin peaksExport and validate one BED row per peak
All 7 recorded steps
  1. Remove adapters and filter paired reads with fastp
  2. Align surviving pairs to hg19 with Bowtie2
  3. Align surviving pairs to hg19 with BWA
  4. Filter for valid MAPQ≥30 non-mitochondrial pairs
  5. Remove PCR duplicates
  6. Call open-chromatin peaks
  7. Export and validate one BED row per peak
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
0.999
Recorded workflow
fastpZip CollectionfastpBowtie2Picard SortsamPicard MarkDuplicates2 more steps
All 8 recorded steps
  1. fastp
  2. Zip Collection
  3. fastp
  4. Bowtie2
  5. Picard Sortsam
  6. Picard MarkDuplicates
  7. SAMtools
  8. MACS2

Score explanation

Minor peak-boundary differences This result follows the calibrated MACS2 BAMPE model protocol. Its peak set is nearly identical to that protocol's reference, with only a few interval differences. Evidence. The output reported 38,769 peaks versus 38,779; 38,750 matched. Precision was 0.999510 and recall was 0.999252.
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp ×2Bowtie2SAMtools ×2Picard MarkDuplicatesMACS2
All 7 recorded steps
  1. fastp
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. SAMtools
  6. Picard MarkDuplicates
  7. MACS2
Galaxy historyHugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
CutadaptfastpBowtie2SAMtoolsPicard MarkDuplicatesMACS2
All 6 recorded steps
  1. Cutadapt
  2. fastp
  3. Bowtie2
  4. SAMtools
  5. Picard MarkDuplicates
  6. MACS2
Galaxy historyHugging Face trace