MultiQC project report
04_reports/multiqc_report.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告TAFFISH REPORT
ngs-qc-flow
Project-level FASTQ quality-control report for short-read NGS data.短读长 NGS FASTQ 数据的项目级质量控制报告。
Executive summary执行摘要
QC Readiness Dashboard质控就绪状态
Use this section first to understand input scale, requested cleaning mode, embedded report availability, and whether detailed review is needed.先看这里可快速了解输入规模、清洗模式、内嵌报告可用性，以及是否需要进一步人工审阅。
Samples2
validated sample rows已验证样本行
FASTQ files3
read files checked已检查 reads 文件
Layout1 PE / 1 SE
paired and single samples双端与单端样本
Cleaningok
fastp modefastp 模式
Embedded reports9
native HTML payloads原生 HTML payload
How to read this report如何阅读本报告
Technical QC first, biological interpretation later.先做技术质控，再谈生物学解释。
This report checks FASTQ-level plausibility and documents how optional cleaning changed the data. It does not prove mapping quality, contamination status, or biological signal.本报告检查 FASTQ 层面的技术合理性，并记录可选清洗如何改变数据；它不证明比对质量、污染状态或生物学信号。
Module status
Inputsok
2 sample(s), 3 FASTQ file(s) validated已验证 2 个样本、3 个 FASTQ 文件
Raw QCok
Raw SeqKit statistics and FastQC reports completed原始 SeqKit 统计和 FastQC 报告已完成
Cleaningok
fastp, clean SeqKit stats, and clean FastQC completedfastp、清洗后 SeqKit 统计和清洗后 FastQC 均已完成
MultiQCok
Native MultiQC report generated原生 MultiQC 报告已生成
Standalone reportok
TAFFISH flow-report template shell and embedded HTML payload index generatedTAFFISH flow-report 模板壳和内嵌 HTML payload 索引已生成
Native HTML resourcesok
No embedded native report declares external render resources没有内嵌原生报告声明外部渲染资源
Workflow
FASTQ QC RouteFASTQ 质控路线
The flow is reference-free and designed as an early checkpoint before RNA-seq, variant, assembly, or other downstream analysis.该流程不依赖参考基因组，适合作为 RNA-seq、变异、组装等下游分析前的早期检查点。
Inputsamples.tsv / FASTQ
->
Raw statsSeqKit
->
Raw QCFastQC
->
Cleaningfastp: ok
->
AggregateMultiQC + TAFFISH report
Embedded subreports
Native QC Reports原生 QC 报告
The buttons open original program-generated HTML reports as separate local pages from payloads stored inside this single report. Resource warnings here are packaging notes for native HTML pages, not sequencing-quality failures.下面的按钮会从当前单个 HTML 文件内保存的 payload 打开原始程序生成的 HTML 报告，并作为独立本地页面显示。这里的资源 WARN 是原生 HTML 页面的打包提示，不代表测序质量失败。
P1_R1_fastqc.html
03_results/raw_fastqc/P1/P1_R1_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告P1_R2_fastqc.html
03_results/raw_fastqc/P1/P1_R2_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告S2_fastqc.html
03_results/raw_fastqc/S2/S2_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告P1.fastp.html
03_results/fastp/P1.fastp.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告S2.fastp.html
03_results/fastp/S2.fastp.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告P1_R1.clean_fastqc.html
03_results/clean_fastqc/P1/P1_R1.clean_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告P1_R2.clean_fastqc.html
03_results/clean_fastqc/P1/P1_R2.clean_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告S2.clean_fastqc.html
03_results/clean_fastqc/S2/S2.clean_fastqc.html
Self-contained by resource scan资源扫描显示为自包含
ok
Open native report打开原生报告| ID | Group | Path | Status | Source bytes | Embedded bytes |
|---|---|---|---|---|---|
| multiqc_1 | multiqc | 04_reports/multiqc_report.html | ok | 2441020 | 2441020 |
| raw_fastqc_2 | raw_fastqc | 03_results/raw_fastqc/P1/P1_R1_fastqc.html | ok | 397683 | 397683 |
| raw_fastqc_3 | raw_fastqc | 03_results/raw_fastqc/P1/P1_R2_fastqc.html | ok | 397683 | 397683 |
| raw_fastqc_4 | raw_fastqc | 03_results/raw_fastqc/S2/S2_fastqc.html | ok | 532489 | 532489 |
| fastp_5 | fastp | 03_results/fastp/P1.fastp.html | ok | 366616 | 366407 |
| fastp_6 | fastp | 03_results/fastp/S2.fastp.html | ok | 185893 | 185684 |
| clean_fastqc_7 | clean_fastqc | 03_results/clean_fastqc/P1/P1_R1.clean_fastqc.html | ok | 397710 | 397710 |
| clean_fastqc_8 | clean_fastqc | 03_results/clean_fastqc/P1/P1_R2.clean_fastqc.html | ok | 397710 | 397710 |
| clean_fastqc_9 | clean_fastqc | 03_results/clean_fastqc/S2/S2.clean_fastqc.html | ok | 532516 | 532516 |
Quality gates
Report-Level Checks报告级检查
These checks summarize whether the flow produced the expected technical evidence.这些检查汇总流程是否产生了预期技术证据。
| Gate | Status | Criterion | Evidence | Impact |
|---|---|---|---|---|
| Input validation | ok | Every declared FASTQ is readable and sample IDs are safe所有声明的 FASTQ 可读取且样本 ID 安全 | 2 sample(s), 3 FASTQ file(s)2 个样本、3 个 FASTQ 文件 | Downstream QC used the intended files下游质控使用了预期文件 |
| Raw QC | ok | Raw FASTQ statistics and FastQC reports are present原始 FASTQ 统计和 FastQC 报告存在 | 03_results/raw_seqkit/raw_fastq_stats.tsv and raw FastQC directory03_results/raw_seqkit/raw_fastq_stats.tsv 和原始 FastQC 目录 | Raw technical quality can be reviewed before filtering可在过滤前审阅原始技术质量 |
| Cleaning | ok | Cleaning outputs match the requested mode清洗产物与请求模式一致 | fastp, clean SeqKit stats, and clean FastQC completedfastp、清洗后 SeqKit 统计和清洗后 FastQC 均已完成 | Users can decide whether clean reads are appropriate for downstream analysis用户可判断 clean reads 是否适合下游分析 |
| Aggregation | ok | MultiQC completed and produced a native HTML reportMultiQC 完成并生成原生 HTML 报告 | 04_reports/multiqc_report.html04_reports/multiqc_report.html | Module-level QC evidence can be inspected interactively可交互检查模块级 QC 证据 |
| Standalone report | ok | Main HTML uses the shared TAFFISH flow-report template contract主 HTML 使用 TAFFISH 共享 flow-report 模板契约 | 9 embedded report payload(s) indexed已索引 9 个内嵌报告 payload | The main HTML can be shared as a single review entry point主 HTML 可作为单文件审阅入口分享 |
| Native HTML resources | ok | Embedded native HTML pages do not declare external render resources内嵌原生 HTML 页面未声明外部渲染资源 | all embedded report payloads self-contained by resource check所有内嵌报告 payload 均通过自包含资源检查 | Embedded native pages should work from the standalone report without adjacent assets内嵌原生页面应可从单文件报告直接打开 |
Sample table
Per-Sample Outputs逐样本输出
The table lists raw inputs and clean FASTQ/report paths generated for each sample.该表列出每个样本的原始输入，以及生成的 clean FASTQ 与报告路径。
| Sample | Layout | Raw R1 | Raw R2 | Clean R1 | Clean R2 | fastp JSON |
|---|---|---|---|---|---|---|
| P1 | paired-end | ngs-qc-flow/testdata/P1_R1.fastq | ngs-qc-flow/testdata/P1_R2.fastq | example-out/03_results/clean_fastq/P1_R1.clean.fastq.gz | example-out/03_results/clean_fastq/P1_R2.clean.fastq.gz | example-out/03_results/fastp/P1.fastp.json |
| S2 | single-end | ngs-qc-flow/testdata/S2.fastq | example-out/03_results/clean_fastq/S2.clean.fastq.gz | example-out/03_results/fastp/S2.fastp.json |
Deliverables
Files to Read, Reuse, and Audit阅读、复用与审计文件
Read firstStandalone report
04_reports/ngs_qc_report.html
Read firstMultiQC
04_reports/multiqc_report.html
ReuseRaw stats
03_results/raw_seqkit/raw_fastq_stats.tsv
ReuseClean stats
03_results/clean_seqkit/clean_fastq_stats.tsv
AuditCommands
04_reports/commands.sh
AuditReport manifest
04_reports/report.manifest.json
| Category | Path | Description |
|---|---|---|
| standalone_report | 04_reports/ngs_qc_report.html | TAFFISH standalone project-level QC report |
| multiqc | 04_reports/multiqc_report.html | Native MultiQC HTML report |
| summary | 04_reports/flow_summary.tsv | Per-sample raw and clean output summary |
| versions | 04_reports/versions.tsv | Flow and dependency versions |
| commands | 04_reports/commands.sh | Executed command provenance |
| run_manifest | run.manifest.json | Machine-readable run manifest |
Methods
Methods, Warnings, and Boundaries方法、警告与边界
QC is a screening layerQC 是筛查层
FastQC, fastp, SeqKit, and MultiQC warnings are technical signals rather than final biological conclusions.FastQC、fastp、SeqKit 和 MultiQC 警告是技术信号，不是最终生物学结论。
Review library type, read length, organism, and downstream task before deciding whether to exclude data.结合建库类型、读长、物种和下游任务再决定是否排除数据。
Embedded QC reports remain native内嵌 QC 报告保持原生形式
The standalone report opens original MultiQC/FastQC/fastp HTML payloads as separate local pages.单文件报告会把原始 MultiQC/FastQC/fastp HTML payload 作为独立本地页面打开。
Keep the full output directory for audit even though the main HTML is shareable alone.即使主 HTML 可单独分享，也建议保留完整输出目录用于审计。
Methods summary
Report templatetaffish-flow-report 0.1.0
The HTML shell, navigation, language switch, and embedded subreport viewer follow the shared TAFFISH template contract.HTML 壳、导航、语言切换和内嵌子报告浏览器遵循 TAFFISH 共享模板契约。
Raw QCSeqKit + FastQC
SeqKit summarizes file-scale statistics; FastQC provides per-file diagnostic modules.SeqKit 汇总文件级统计；FastQC 提供单文件诊断模块。
Cleaningfastp
When requested, fastp generates cleaned reads and native JSON/HTML reports.启用清洗时，fastp 生成 clean reads 和原生 JSON/HTML 报告。
AggregationMultiQC
MultiQC collects module outputs into a native project-level HTML report and data bundle.MultiQC 将各模块输出汇总为原生项目级 HTML 报告和数据包。
Review boundarytechnical QC
This flow does not perform contamination screening, reference mapping, or biological interpretation.本流程不执行污染筛查、参考基因组比对或生物学解释。
Glossary
FASTQ
Text format containing sequencing reads and per-base quality scores包含测序 reads 及逐碱基质量分数的文本格式
FastQC
Per-file quality-control program for common sequencing quality patterns用于检查常见测序质量模式的单文件质控程序
fastp
Read preprocessing tool for adapter trimming, quality filtering, and clean-read reporting用于接头剪切、质量过滤和 clean-read 报告的 reads 预处理工具
MultiQC
Aggregator that collects many bioinformatics QC outputs into one report将多个生信 QC 输出汇总为一个报告的聚合工具
Standalone HTML
A report whose main CSS, JavaScript, and embedded QC payload index are stored in one HTML file主 CSS、JavaScript 和内嵌 QC payload 索引存于同一个 HTML 文件中的报告
Provenance
Audit Trail审计溯源
The full output directory keeps logs, native reports, commands, versions, manifests, and machine-readable indexes beside this standalone HTML.完整输出目录保留日志、原生报告、命令、版本、manifest 和机器可读索引，并与本单文件 HTML 并列保存。
| File | Role |
|---|---|
| run.manifest.json | run manifest |
| 04_reports/report.manifest.json | report manifest |
| 04_reports/commands.sh | commands |
| 04_reports/versions.tsv | versions |
| 04_reports/embedded_html_reports.tsv | embedded HTML payload index |