Manually test out new ARM setup for drugresponseeval

[ewels]

Try setting up arch64 / arm built containers for the pipeline with the new Seqera Containers infrastructure.

Can do this manually in this pipeline to test out functionality.

See also https://github.com/nf-core/testpipeline/pull/139/files which was a similar effort, but for the testpipeline.

[vagkaratzas]

Opened a draft PR with the amd64 container that works for most of the pipeline, except for the first few unzipping modules.
@JudithBernett can you use the existing nf-core modules for unzipping instead of your local ones (e.g., unzip, or anything else in nf-core that would cover your case)? Then it will be way easier to implement the container configurations including those as well.

Will do the arm ones tomorrow.

[vagkaratzas]

The PR has been merged. @JudithBernett if you have access to a system using ARM, let us know if the containers work as intended. For conda tests failing, try upgrading minimum Nextflow version for pipeline to 25.04.8.

[JudithBernett]

Successfully tested on a Mac M1 Chip, Nextflow 25.10.2
nextflow run . <...>

• -profile test,mamba_arm
• -profile test,conda_arm
• -profile test,docker_arm

Cannot test singularity_arm, apptainer_arm, singularity_oras_arm, apptainer_oras_arm because singularity/apptainer does not have Mac support.

[mashehu]

RNA-seq has arm CI tests, if you want to do more thorough tests.
https://github.com/nf-core/rnaseq/blob/master/.github/workflows/nf-test-arm.yml
(for now I would only have on: workflow_dispatch as the only trigger for that github action, to not run too many things

[JudithBernett]

nice! But wouldn't this: https://github.com/nf-core/rnaseq/blob/759dbf125280e6faeaa4194dd74f872d224fc327/.github/workflows/nf-test-arm.yml#L74

have to be docker_arm then?
@mashehu

[mashehu]

correct, rnaseq doesn't have the new config setup.

[JudithBernett]

I tried to add it to my workflows @mashehu (with docker_arm), but it fails to publish the downloaded file … did you have similar issues? (https://github.com/nf-core/drugresponseeval/actions/runs/20027667276/job/57428889352?pr=70)

ERROR ~ Failed to publish file: /home/runner/_work/drugresponseeval/drugresponseeval/~/tests/77dca59bee2e19e5ecd52769bdf5abc8/work/72/a7efc87c76036ac94ed55dc6d0d244/meta; to: /home/runner/_work/drugresponseeval/drugresponseeval/~/tests/77dca59bee2e19e5ecd52769bdf5abc8/data/meta [copy] -- See log file for details

I don't have this issue locally with nf-test test --profile=+docker_arm --verbose

[mashehu]

works now in #80