A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi <!channel>,
I’d appreciate your advice on a CI issue with my PR connecting *GATK → BCFtools consensus → MAFFT → IQ-TREE*.
The PHYLOGENY test passes locally with Nextflow 25.10.4 and Docker, but the GitHub Actions test fails before execution because of a syntax issue in the existing `conf/modules.config`.
I haven't modified that configuration because it is outside the scope of my PR. Would you recommend addressing this separately or taking another approach?
Thanks for your guidance!

Yes, thanks! Here is the failed <https://github.com/nf-core/pathogenepidemiology/actions/runs/37795072065|CI run>. The relevant failure is in `docker | 25.10.4 | 2/2`. The log shows a syntax error in the existing `conf/modules.config` before the PHYLOGENY test could execute.
Thanks for taking a look!

Ah, sorry if I introduced that. If you find out what the module config issue is, make a note of it in something like a PR comment in case we can learn from it

Hi Bilal, How is everything from your side? no worries! I've already added a comment to the PR documenting the configuration issue, the CI failure, and the successful local test after temporarily replacing the line. I haven't changed `conf/modules.config` in my PR.
Thanks!

Still recovering, it's not so nice :sweat_smile: but it has gone relatively well thanks. I'll let you know how I am on Monday

I tested both `DOWNLOAD_REFFASTA` and `PHYLOGENY` locally using Nextflow 25.10.4. Both tests passed after I temporarily replaced the problematic line in `conf/modules.config` with `cpus = 4`.
I then restored the original configuration, so no unrelated changes are included in my PR. This suggests that the CI failures are caused by the existing configuration issue rather than these two tests.
Thanks for your guidance!

I'll take a look at everything today after catching up on some errands I wasn't fit for last week