Catalog Retrieval 回放
构建一个 bulk RNA-seq 差异表达分析工作流，输入多个样本的 paired-end FASTQ 文件。每个样本先运行 fastp 做读段质控，再用 Salmon 做转录本定量，随后通过 tximport 汇总到基因层面，用 DESeq2 完成差异表达分析，并返回 MultiQC 质控报告。
Matched approved catalog recipe fields (name, aliases, description, required_inputs.description) using terms: rna, seq, bulk, fastq, salmon, fastp.
Matched approved catalog tool fields (id, aliases, description, inputs.description) using terms: salmon, rna, seq, fastq, multiqc.
Matched approved catalog tool fields (id, aliases, description, inputs.description) using terms: fastp, fastq, multiqc.
Matched approved catalog tool fields (id, aliases, description, inputs.description) using terms: tximport, salmon.
Matched approved catalog tool fields (id, description, inputs.description, outputs.name) using terms: multiqc.
Matched approved catalog tool fields (id, runtime.docker) using terms: deseq2.
请求内容
Natural-language request
构建一个 bulk RNA-seq 差异表达分析工作流，输入多个样本的 paired-end FASTQ 文件。每个样本先运行 fastp 做读段质控，再用 Salmon 做转录本定量，随后通过 tximport 汇总到基因层面，用 DESeq2 完成差异表达分析，并返回 MultiQC 质控报告。
诊断摘要
失败回放
Run 未成功完成；这里汇总持久化 snapshot 中保留下来的失败线索和结构化产物。
❌ WDL 语法校验失败！校验器：miniwdl。请根据以下错误信息反思并重新输出修改后的完整代码： (generated.wdl Ln 52 Col 5) Value/call name collision on multiqc_report File multiqc_report = multiqc_report.multiqc_report ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
DAG 展示失败前已经保存的 Workflow IR 结构；失败阶段以事件时间线和 diagnostics 为准，不映射成 workflow call 执行状态。
Recipe Tool Plan
DAG 可视化输入
Renderer 输出
Analyzer 与 checker 记录
Workflow DAG
基于 Workflow IR 的 inputs、steps、scatter 和 outputs 构建依赖图；该图展示编译时结构，不代表真实任务执行状态。
事件时间线
事件来自持久化 SSE envelope，可用于回放 run 的关键阶段。
结构化产物
Plan、Workflow IR、WDL 与诊断来自持久化 run snapshot。
{
"workflow": {
"inputs": {
"raw_r1s": "Array[File]",
"raw_r2s": "Array[File]",
"sample_groups": "File",
"sample_ids": "Array[String]",
"transcriptome_index": "File",
"tx2gene": "File"
},
"name": "BulkRNASeqDifferentialExpression",
"outputs": {
"deg_table": "deseq2_de.deg_table",
"multiqc_report": "multiqc_report.multiqc_report"
},
"recipe": "rnaseq_differential_expression",
"tool_calls": [
{
"id": "fastp_qc",
"inputs": {
"r1": "raw_r1s",
"r2": "raw_r2s"
},
"params": {},
"step": "qc",
"tool": "fastp",
"version": "1.3.3"
},
{
"id": "salmon_quant",
"inputs": {
"index": "transcriptome_index",
"r1": "fastp_qc.clean_r1",
"r2": "fastp_qc.clean_r2"
},
"params": {},
"step": "quantify",
"tool": "salmon",
"version": "1.9.0"
},
{
"id": "tximport_summarize",
"inputs": {
"quant_files": "salmon_quant.quant_file",
"sample_ids": "sample_ids",
"tx2gene": "tx2gene"
},
"params": {},
"step": "summarize_transcripts",
"tool": "tximport",
"version": "1.30.0"
},
{
"id": "deseq2_de",
"inputs": {
"counts": "tximport_summarize.gene_counts",
"sample_groups": "sample_groups"
},
"params": {},
"step": "differential_expression",
"tool": "deseq2",
"version": "1.42.1"
},
{
"id": "multiqc_report",
"inputs": {},
"params": {},
"step": "qc_report",
"tool": "multiqc",
"version": "1.21"
}
]
}
}