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

nf-core

I'm finding the entrypoint of `<http://quay.io/nf-core/proteinfold_alphafold2_standard:2.0.0|quay.io/nf-core/proteinfold_alphafold2_standard:2.0.0>` is triggering Alphafold which breaks Nextflow. Is there one without this I can use? I don't think I can override the entrypoint in my runtime

The previous version `1.1.1` had not entry point, although there has been some updates since then, as I don’t know the context maybe this is silly but couldn’t you use the `stub` run instead?

:thinking_face: just out of curiosity, why you want to run the pipeline without triggering alphafold?

I can't use stubrun because I want to actually fold some proteins :laughing:

&gt; why you want to run the pipeline without triggering alphafold?
It breaks Nextflow?

I just get a command error instead of running Alphafold

umm, strange I run it yesterday using the same image and it worked, which is the error?

you are basically trying to run this command:

```alphafold2 .command.run```

&gt; I run it yesterday using the same image
Where did you run it?

Right, that's going to override the entrypoint for you

If you check .command.run, you'll find it says `docker run --entrypoint ""`

But on other systems, it runs `.command.run`  within the Docker image, so the entrypoint has already executed

I am using apptainer:
```apptainer exec --no-home --pid -B /users/cn/jespinosa --nv /users/cn/jespinosa/nxf_singuarlity_cachedir/quay.io-nf-core-proteinfold_alphafold2_standard-2.0.0.img /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); bash -C -e -u -o pipefail /users/cn/jespinosa/scratch/final_test/48/e903b98be66baaf6457b8865a3b4ac/.command.run nxf_trace"```

I believe `apptainer exec` bypasses the entrypoint?

Anyway, remove the entrypoint, it achieves nothing :laughing:

Not tested but you may want to try something such as: `containerOptions '--entrypoint /bin/bash'` and try to overwrite it in the meanwhile

yep that's what I've been doing and it seems to work, but it's a pain because it breaks other stuff

:point_right::skin-tone-2: <https://github.com/nf-core/proteinfold/pull/500>

The images are already available under the 2.0.0 tag