Reporting报告生成

rnaseq-report-flow

This flow is a static collection and interpretation layer. Version 0.2.0-r2 supports both reference and de novo standard-flow outputs, gathers plots, tables, linked QC HTML, commands, versions, methods, and manifests, then renders a bilingual report and a longer interpretation guide.

rnaseq-report-flow 0.2.0-r2 是静态收集和解读层，同时支持有参和无参 standard-flow 输出。它收集图、表、QC HTML 链接、命令、版本、方法和 manifest，并生成双语主报告与长文解读指南。

0.2.0-r2Reference and de novo delivery layer有参与无参交付层GitHub

Collect a standard-flow run

收集标准流程结果

taf-rnaseq-report-flow \
  --standard-out rnaseq-standard-out \
  --project-name "RNA-seq project" \
  --outdir report-out

Collect separate subflows

收集独立子流程

taf-rnaseq-report-flow \
  --expression-out expression-out \
  --de-out de-out \
  --enrichment-out enrichment-out \
  --denovo-assembly-out denovo-assembly-out \
  --denovo-expression-out denovo-expression-out \
  --denovo-annotation-out denovo-annotation-out \
  --analysis-mode denovo \
  --outdir report-out

Input requirements

输入要求

Pass either --standard-out or one or more upstream flow output directories. The report flow reads existing outputs; it does not rerun quantification, assembly, DE, enrichment, or QC.

可以传入 --standard-out，也可以传入一个或多个上游流程输出目录。报告流程只读取已有结果，不重新运行定量、组装、差异分析、富集或 QC。

Reference modules

有参模块

--reference-out, --expression-out, --alignment-out, --count-out, --alignment-qc-out, --de-out, and --enrichment-out.

--reference-out、--expression-out、--alignment-out、--count-out、--alignment-qc-out、--de-out 和 --enrichment-out。

De novo modules

无参模块

--denovo-assembly-out, --denovo-expression-out, --denovo-annotation-out, plus --de-out and optional --enrichment-out.

--denovo-assembly-out、--denovo-expression-out、--denovo-annotation-out，再加上 --de-out 和可选 --enrichment-out。

Parameter reference

参数说明

ParameterRequiredDefaultMeaning
--outdir, -oyesnoneDedicated report output directory; existing outputs are refused unless --force is used.专用报告输出目录；已有目录默认拒绝，除非使用 --force。
--standard-outone inputnoneCompleted standard-flow output. Preferred for full end-to-end reports because it auto-discovers modules.完整 standard-flow 输出目录。端到端报告优先使用，因为它会自动发现模块。
--reference-out, --expression-out, --alignment-out, --count-out, --alignment-qc-outoptionalnoneReference route module directories when subflows were run separately.单独运行有参子流程时传入对应模块目录。
--denovo-assembly-out, --denovo-expression-out, --denovo-annotation-outoptionalnoneDe novo module directories for assembly, transcript quantification, and annotation sections.无参组装、转录本定量和注释章节使用的模块目录。
--de-out, --enrichment-outoptionalnoneStatistical result modules. Enrichment may be absent in expression-only or annotation-limited runs.统计结果模块。表达矩阵-only 或注释不足运行中 enrichment 可能不存在。
--analysis-modeoptionalautoReport label: reference, denovo, or auto-detected from standard-flow summaries.报告展示标签：reference、denovo，或从 standard-flow 摘要自动识别。
--analysis-route, --de-sourceoptionalautoHuman-readable route and count-source labels shown in the overview.总览中展示的人类可读路线和计数来源标签。
--project-namenoRNA-seq projectReport title and project label.报告标题和项目名称。
--forcenooffReplace standard report outputs inside an existing output directory.允许替换已有输出目录中的标准报告结果。

Key outputs and limits

关键输出与边界

Primary outputs are 04_reports/rnaseq_report.html, 04_reports/report_interpretation.html, plot/table indexes, copied or linked HTML reports, command/version summaries, and provenance records. The flow does not change upstream results; it organizes them by biological question and preserves links to supporting files.

主要输出是 04_reports/rnaseq_report.html、04_reports/report_interpretation.html、图表索引、复制或链接的 HTML 子报告、命令/版本摘要和溯源记录。这个流程不会修改上游结果；它按生物学问题组织结果，并保留到支持文件的链接。