pipeline_report.{txt,html} missing from pipeline_info directory

[ChristopherBarrington]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/rnaseq pipeline documentation

Description of the bug

The pipeline_report.txt file is not written by v3.3

Expected behaviour

In previous versions the pipeline_info/pipeline_report.txt file contained (pretty much) the top lines of the output of the pipeline with each parameter listed.

System

I am using -profile crick

Nextflow Installation

• Version:21.04.0

Container engine

• Engine: Singularity
• version: 3.4.2

Additional context

I checked in the rnaseq repo for where the file is written but could not see it. I'm not sure if it is part of the nf-core/tools repo and how those parts of nfcore work together with the DSL2 version?

[drpatelh]

Thanks for reporting @ChristopherBarrington. So these files are created but only if you provide --email / --email_on_fail. The metrics that are dumped to those files are a byproduct of creating all of the info required to generate and send the email. This email code has required refactoring for the longest time (see nf-core/tools#112) so this is the best we can do for now :)

I have clarified this in the docs too drpatelh@8a558d3

[ChristopherBarrington]

That makes sense, I had omitted that option for this run simply to avoid getting the email. But it's a small price to pay to get the parameter information recorded.

Thank you