IWC benchmark item

wf_001_short_read_qc_trim

Short-read quality control and trimming

Short-read quality control and trimming (SRR1553606)

Open source IWC workflowGround-truth Galaxy history

Reference workflow

2 tool steps across 2 unique tools, including tools inside nested subworkflows. A plus sign denotes parallel branches.

Workflow
fastpMultiQC

Complete query

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

Perform paired-end quality control and trimming on the provided Illumina reads.
Detect and remove adapters solely through mate-overlap analysis, without supplying an adapter sequence or running a separate adapter-sequence autodetection step. Treat bases below Phred 20 as low quality. Discard the pair if either mate contains more than 40 percent low-quality bases, more than 5 ambiguous `N` bases, or is shorter than 15 bases after adapter trimming. Do not perform any other trimming or base correction.
Write the synchronized retained mates to `final_answer/trimmed_forward.fastqsanger.gz` and `final_answer/trimmed_reverse.fastqsanger.gz`.

acc evaluator

acc compares the final output files with the reference outputs.

Metric
paired_fastq_f1
Definition

Transformation-aware paired FASTQ score that emphasizes which reads were filtered or trimmed while also checking retained read identities.

Formula
Final scoreS = √(F1(M_T, C_T, R_T) × F1(M_ID, C_ID, R_ID))

Geometric mean of transformation agreement and retained-read-ID agreement.

F1F1(M,C,R) = 2M/(C+R)

Equivalent to 2PR/(P+R), where P=M/C and recall=M/R; if C=R=0, F1=1.

Transform matchM_T = Σᵢ tᵢ; tᵢ = 1 if both remove the pair, √(J_F J_R) if both retain a changed pair, otherwise 0

C_T and R_T are the numbers of input pairs changed or removed by the candidate and reference.

Mate similarityJ_m = max |I_C ∩ I_R| / |I_C ∪ I_R|

I_C and I_R are candidate and reference contiguous sequence-and-quality slices of the same input mate.

Retained IDsM_ID = |ID_C ∩ ID_R|; C_ID = |ID_C|; R_ID = |ID_R|

Read-pair IDs are the matching units.

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 adapters from paired reads using mate-overlap analysis.
    • A successful paired-read adapter-removal execution used mate-overlap adapter detection.
    • The successful execution produced paired outputs consumed by the filtering/final-output chain.
  2. Step 2Apply the Q20, 40%-low-quality-base, 5-N, and 15-base rules to whole pairs; keep mates synchronized and make no other trimming or base corrections.
    • The successful execution applied Q20, at most 40% low-quality bases, at most 5 N bases, and minimum length 15.
    • Pair-level retention kept forward and reverse mates synchronized.
    • No additional quality trimming, poly-G/poly-X trimming, or base correction changed retained reads.
    • Both required trimmed FASTQ artifacts exist and pass the final-answer artifact checks.

Model results and score explanations

The 5 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
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringCutadapt adapter removalValidate synchronized paired FASTQ outputs
All 3 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Cutadapt adapter removal
  3. Validate synchronized paired FASTQ outputs
Hugging Face trace

Galaxy-API code

GPT-5.6 Sol

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace

Galaxy-API code

GPT-5.6 Luna

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringCutadapt adapter removalValidate synchronized paired FASTQ outputs
All 3 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Cutadapt adapter removal
  3. Validate synchronized paired FASTQ outputs
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Input validation — Table transformationTrim and filter — fastpPost trim validationFinal scope check — Table transformationFinal audit — Table transformation
All 5 recorded steps
  1. Input validation — Table transformation
  2. Trim and filter — fastp
  3. Post trim validation
  4. Final scope check — Table transformation
  5. Final audit — Table transformation
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Input inspectionTool discovery — fastpTool search — fastpParameter confirmation — fastpTrim and filter overlap only — fastpOutput pair validation overlap only2 more steps
All 8 recorded steps
  1. Input inspection
  2. Tool discovery — fastp
  3. Tool search — fastp
  4. Parameter confirmation — fastp
  5. Trim and filter overlap only — fastp
  6. Output pair validation overlap only
  7. Raw prefix provenance validation overlap only
  8. Final delivery validation overlap only
Hugging Face trace

Galaxy-API code

R2acc · step score 1.000
0.996
Recorded workflow
fastpZip CollectionfastpUnzip Collection
All 4 recorded steps
  1. fastp
  2. Zip Collection
  3. fastp
  4. Unzip Collection

Score explanation

Adapter-detection setting A separate paired-end adapter autodetection option was enabled even though the task required mate-overlap-only adapter detection. That extra decision path changed both which pairs survived and which reads were trimmed. Evidence. Among 377,961 input pairs, the output had 63 extra and 561 missing retained-pair IDs. Its trimming/removal decisions had 1,664 extra and 63 missing pairs.
Galaxy historyHugging Face trace
R3acc · step score 1.000
0.998
Recorded workflow
fastp ×2
All 2 recorded steps
  1. fastp
  2. fastp

Score explanation

Adapter-detection setting A separate paired-end adapter autodetection option was enabled even though the task required mate-overlap-only adapter detection. That extra decision path changed both which pairs survived and which reads were trimmed. Evidence. Among 377,961 input pairs, the output had 93 extra and 1 missing retained-pair ID. Its trimming/removal decisions had 1,082 extra and 93 missing pairs.
Galaxy historyHugging Face trace

Codex + DeepSeek V4 Pro

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringCutadapt adapter removalValidate synchronized paired FASTQ outputs
All 3 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Cutadapt adapter removal
  3. Validate synchronized paired FASTQ outputs
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
fastp overlap adapter removal and pair filteringValidate synchronized paired FASTQ outputs
All 2 recorded steps
  1. fastp overlap adapter removal and pair filtering
  2. Validate synchronized paired FASTQ outputs
Hugging Face trace
R3acc · step score 1.000
0.996
Recorded workflow
Fastp overlap adapter trimPair filter — Filter rowsValidate outputs
All 3 recorded steps
  1. Fastp overlap adapter trim
  2. Pair filter — Filter rows
  3. Validate outputs

Score explanation

Adapter-detection setting The run used fastp's mate-overlap adapter trimming together with a separate pair-filtering step. That combination changed a small fraction of the retained pairs and trimming decisions relative to the reference. Evidence. Among 377,961 input pairs, the output had 561 missing retained-pair IDs and no additional IDs. Its trimming/removal decisions had 1,664 additional and 63 missing pairs.
Hugging Face trace

Galaxy-API code

R2acc · step score 1.000
0.996
Recorded workflow
fastp ×2
All 2 recorded steps
  1. fastp
  2. fastp

Score explanation

Adapter-detection setting A separate paired-end adapter autodetection option was enabled even though the task required mate-overlap-only adapter detection. That extra decision path changed both which pairs survived and which reads were trimmed. Evidence. Among 377,961 input pairs, the output had 63 extra and 561 missing retained-pair IDs. Its trimming/removal decisions had 1,664 extra and 63 missing pairs.
Galaxy historyHugging Face trace
R3acc · step score 1.000
0.996
Recorded workflow
fastp
All 1 recorded steps
  1. fastp

Score explanation

Adapter-detection setting A separate paired-end adapter autodetection option was enabled even though the task required mate-overlap-only adapter detection. That extra decision path changed both which pairs survived and which reads were trimmed. Evidence. Among 377,961 input pairs, the output had 63 extra and 561 missing retained-pair IDs. Its trimming/removal decisions had 1,664 extra and 63 missing pairs.
Galaxy historyHugging Face trace