Reporting

Last updated on 2025-06-27 | Edit this page

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Overview

Questions

  • How do I get information about my pipeline run?
  • How can I see what commands I ran?
  • How can I create a report from my run?

Objectives

  • View Nextflow pipeline run logs.
  • Use nextflow log to view more information about a specific run.
  • Create an HTML report from a pipeline run.

Nextflow log

Once a script has run, Nextflow stores a log of all the workflows executed in the current folder. Similar to an electronic lab book, this means you have a record of all processing steps and commands run.

You can print Nextflow’s execution history and log information using the nextflow log command.

This will print a summary of the executions log and runtime information for all pipelines run. By default, included in the summary, are the date and time it ran, how long it ran for, the run name, run status, a revision ID, the session id and the command run on the command line.

Task 9.1

Listing the execution logs of previous invocations of all pipelines in a directory.

BASH 

$ nextflow log

The output will look similar to this:

OUTPUT 

TIMESTAMP               DURATION        RUN NAME                STATUS  REVISION ID     SESSION ID                        COMMAND
2025-04-12 17:56:01     3.2s            disturbed_bartik        OK      8a3d1bb9c7      09de2950-9894-4463-b55b-4afa4268a3e2    nextflow run read_data.nf

If we want to get more information about a timeline we can request a timeline or report to be outputted to the docs/ folder in our repository.

Task 9.2

Output a report.

GROOVY 


report {
  // there is some isse with ps not being available in the container So I wanted to ask if you see the possibility to include ps in your docker container so that it can be used with nextflow (had only a problem with missing ps, but all others seem available, i.e. awk, date, grep, egrep, sed, tail, tee).
  enabled = true
  overwrite = true
  file = "${projectDir}/docs/report.html"
}

This will list the set of tasks and the time and memory resources these required to be completed. Additionally, further information is included on the command used to launch the pipeline, the output directory, and the status of each job submission, i.e whether this was Cached (run previously), Succeeded or Failed.

Information is included on the timeline of tasks scheduled as part of the pipeline.

Task 9.3

Output a timeline.

GROOVY 


timeline {
  enabled = true
  overwrite = true
  file = "${projectDir}/docs/timeline.html"
}

Key Points

  • Nextflow can produce a custom execution report with run information using the log command.
  • You can generate a report or timeline using the template specified by Nextflow.