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Update Reports overview page #665

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Update Reports overview page
justinegeffen Jun 10, 2025
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Merge branch 'master' into justinegeffen-reports
justinegeffen Jul 14, 2025
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15 changes: 7 additions & 8 deletions platform-cloud/docs/reports/overview.md
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Expand Up @@ -2,20 +2,20 @@
title: "Reports"
description: "Overview of pipeline reports in Seqera Platform."
date: "24 Apr 2023"
tags: [pipeline, schema]
tags: [pipeline, schema, reports, metrics, logs]
---

Most Nextflow pipelines will generate reports or output files which are useful to inspect at the end of the pipeline execution. Reports may be in various formats (e.g. HTML, PDF, TXT) and would typically contain quality control (QC) metrics that would be important to assess the integrity of the results.

**Reports** allow you to directly visualise supported file types or to download them via the user interface (see [Limitations](#limitations)). This saves users the time and effort of having to retrieve and visualize output files from their local storage.
**Reports** allow you to directly visualise supported file types or to download them via the user interface (see [Limitations](#limitations)). This saves you the time and effort of having to retrieve and visualize output files from their local storage.

### Visualize reports

Available reports are listed in a **Reports** tab on the **Runs** page. You can select a report from the table to view or download it (see [Limitations](#limitations) for supported file types and sizes).

To open a report preview, the file must be smaller than 10 MB.

You can download a report directly or from the provided file path. Reports larger than 25MB cannot be downloaded directly — the option to download from file path is given instead.
You can download a report directly or from the provided file path. Reports larger than 25 MB cannot be downloaded directly — the option to download from file path is given instead.

### Configure reports

Expand All @@ -32,9 +32,9 @@ Any configuration provided in the interface will override configuration supplied

### Configure reports for Nextflow CLI runs

The reports and log files for pipeline runs launched with Nextflow CLI (`nextflow run <pipeline> -with-tower`) can be accessed directly in the Seqera UI. The files generated by the run must be accessible to your Seqera workspace primary compute environment. Specify your workspace prior to launch by setting the `TOWER_WORKSPACE_ID` environment variable. Reports are listed under the **Reports** tab on the run details page.
The reports and log files for pipeline runs launched with Nextflow CLI (`nextflow run <pipeline> -with-tower`) can be accessed directly in Platform. The files generated by the run must be accessible to your workspace's primary compute environment. Specify your workspace prior to launch by setting the `TOWER_WORKSPACE_ID` environment variable. Reports are listed under the **Reports** tab on the run details page.

Execution logs are available in the **Logs** tab by default, provided the output files are accessible to your workspace primary compute environment. To specify additional report files to be made available, your pipeline repository root folder must include a `tower.yml` file that specifies the files to be included (see below).
Execution logs are available in the **Logs** tab by default, provided the output files are accessible to your workspace's primary compute environment. To specify additional report files to be made available, your pipeline repository root folder must include a `tower.yml` file that specifies the files to be included (see below).

### Reports implementation

Expand All @@ -49,7 +49,7 @@ reports:

### Path pattern

Only the published files (using the Nextflow `publishDir` directive) are candidate files for Seqera reports. The path pattern is used to match published files to a report entry. It can be a partial path, a glob expression, or just a file name.
Only the published files (using the Nextflow `publishDir` directive) are candidate files for reports. The path pattern is used to match published files to a report entry. It can be a partial path, a glob expression, or just a file name.

Examples of valid path patterns are:

Expand Down Expand Up @@ -87,7 +87,7 @@ Nextflow can generate a number of built-in reports:
- [Trace file](https://nextflow.io/docs/latest/tracing.html#trace-report)
- [Workflow diagram](https://nextflow.io/docs/latest/tracing.html#dag-visualisation) (i.e. DAG)

In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Seqera Platform. Specify them in `tower.yml` like any other file:
In Nextflow version 24.03.0-edge and later, these reports can be included as pipeline reports in Platform. Specify them in `tower.yml` like any other file:

```yaml
reports:
Expand All @@ -108,7 +108,6 @@ The filenames must match any custom filenames defined in the Nextflow config:
- Execution timeline: `timeline.file`
- Trace file: `trace.file`
- Workflow diagram: `dag.file`

:::

### Limitations
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