How to fix multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'. ?

[olgabot]

Description of the bug

Hello,
I am writing an internal pipeline and got the error message: multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

My report_comment is:

report_comment: >
  This report has been generated by the <a href="https://github.com/BridgeBioAnalytics/nf-core-pipelinename/1.0dev" target="_blank">nf-core/pipelinename</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/pipelinename/1.0dev/output" target="_blank">documentation</a>.

It's the only error that is causing my PR to fail, and I don't know how to fix it. The one little red "x" that won't go away! And my dopamine wants that green check mark to merge the PR.

Grateful for your help!
Thank you.
Olga

Command used and terminal output

$ nf-core lint
... warnings ...

╭─ [✗] 1 Pipeline Test Failed ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                        │
│ multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.                                                                                              │
│                                                                                                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 330 Tests Passed  │
│ [?]   0 Tests Ignored │
│ [!]  74 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯

System information

• Nextflow version: 23.04.2 build 5870
• Hardware: EC2 instance and GitHub Actions
• Executor: local and GitHub Actions
• OS: Linux (Linux ip-172-31-3-24.us-west-1.compute.internal 4.14.314-238.539.amzn2.x86_64 #1 SMP Tue May 23 16:44:05 UTC 2023 x86_64 GNU/Linux from uname -a)
• Version of nf-core/tools: 2.10
• Python version: Python 3.10.12

[lpantano]

same here in nf-core/smrnaseq#281

[apeltzer]

I had this once or twice too, but mostly this was because I modified the file from the original template version:

https://raw.githubusercontent.com/nf-core/tools/master/nf_core/pipeline-template/assets/multiqc_config.yml

After adding this back in "cleanly", it worked for me. (had the same in nanostring)

[apeltzer]

Ok, found the problem (for smrnaseq at least). The Branch mirtop-gff contained a release 2.4.4 version number which was not containing a dev. If you merge to dev, it should have a dev attached to version, otherwise the report statement is not considered correct.

nf-core bump-version 2.4.4dev updated both the nextflow.config and the multiqc_config.yml with an appropriate report_comment and then things were linting fine 👍🏻

Note for myself: Only add a version number without dev when you already are on dev.

[olgabot]

@apeltzer My pipeline doesn't have a version number 🙈 .. does that mean it won't work until I add a Git tag with a version number and sync it to the MultiQC Config yaml?

[mashehu]

The error comes from these lines in the linting code:
https://github.com/nf-core/tools/blob/master/nf_core/lint/multiqc_config.py#L73-L86

If you add 1.0dev to the manifest section of your nextflow.config file it should resolve itself.

[lpantano]

Thank you!, It got mention in our issue. I will remember for next time.

[olgabot]

I think I figured it out. 4 months ago, the URL structure was changed, which was probably reflected in the latest 2.10 release.

However, I still can't get this test to pass.

Changing the multiqc_config.yml file

In the multiqc_config.yml file, I changed:

• https://github.com/nf-co.re/pipelinename/1.0dev to https://github.com/nf-co.re/pipelinename/releases/tag/1.0dev
• https://nf-co.re/pipelinename/1.0dev/output to https://nf-co.re/pipelinename/1.0dev/docs/output

but still have had no luck. The context of the changes is below.

report_comment: >
  This report has been generated by the <a href="https://github.com/nf-co.re/pipelinename/1.0dev" target="_blank">nf-core/aav</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/pipelinename/1.0dev/output" target="_blank">documentation</a>.

to

report_comment: >
  This report has been generated by the <a href="https://github.com/nf-co.re/pipelinename/releases/tag/1.0dev" target="_blank">nf-core/pipelinename</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/pipelinename/1.0dev/docs/output" target="_blank">documentation</a>.

Ignoring the test

I've also tried to ignore this test, and can't seem to get the .nf-core.yml file configured properly to ignore the report_comment test

I've tried:

repository_type: pipeline
lint:
  multiqc_config: False
  report_comment: False

And:

repository_type: pipeline
lint:
  multiqc_config:
    report_comment: False

Can you help me understand what is the right syntax to ignore this test?

[mashehu]

Slight error with the github org url and the name of the pipeline in your report. It should be :

- This report has been generated by the <a href="https://github.com/nf-co.re/pipelinename/releases/tag/1.0dev" target="_blank">nf-core/pipelinename</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/pipelinename/1.0dev/docs/output" target="_blank">documentation</a>.
+ This report has been generated by the <a href="https://github.com/nf-core/NAME_OF_YOUR_PIPELINE/releases/tag/1.0dev" target="_blank">nf-core/NAME_OF_YOUR_PIPELINE</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/NAME_OF_YOUR_PIPELINE/1.0dev/docs/output" target="_blank">documentation</a>.

[olgabot]

Slight error with the github org url and the name of the pipeline in your report. It should be :

- This report has been generated by the <a href="https://github.com/nf-co.re/pipelinename/releases/tag/1.0dev" target="_blank">nf-core/pipelinename</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/pipelinename/1.0dev/docs/output" target="_blank">documentation</a>.
+ This report has been generated by the <a href="https://github.com/nf-core/NAME_OF_YOUR_PIPELINE/releases/tag/1.0dev" target="_blank">nf-core/NAME_OF_YOUR_PIPELINE</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/NAME_OF_YOUR_PIPELINE/1.0dev/docs/output" target="_blank">documentation</a>.

Thanks for the catch, @mashehu! I changed github.com/nf-co.re -> github.com/nf-core but my tests are still failing :( Is there a way to ignore this test for now?

[olgabot]

Turns out I was editing the wrong .nf-core.yml file 😅

This version does work!

repository_type: pipeline
lint:
  multiqc_config:
    report_comment: False