Comments (5)
Okay okay @MarieLataretu @hoelzer @replikation, I'll have to look into how this works with profiles + nxf but I'll give it an attempt.
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Agree, but maybe the "test profile" Option as mentioned by @replikation could be an interesting use case @Krannich479 . "test_vcf" could download simulated example data and a "gold standard" vcf and then let's porecov produce a new vcf which then can be compared.
Might be neat to test new medaka versions and models.
The test run would then happen outside any GitHub action locally
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I would prefer to run automatic complete tests via git action, but the question would be, who is financing this ;)? We added test profiles so we run outside GH Action test runs. Important containers are tested directly with real data prior to deployment. So the workflow logic is tested, and some of the important containers are.
Also, since the workflow uses containerization, it would need to download and run multiple containers, which would require more space for the gitaction runs, I think.
But maybe I misunderstood what you mean by benchmark. we could always add such tests to out test profile runs. (listed in the --help
Lines 559 to 563 in ff6cb14
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Valid points. When I came up with this idea I totally forgot that poreCov is deploying a number of containers that in total might exceed the GH Actions runner's resources. Also, the most relevant aspect to me is the variant calling which (I just found out) has a quite elaborate test suite within the ARTIC pipeline. I'll close this issue for now.
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Yes, I agree with @hoelzer; it'd still be useful and interesting outside of GH!
We have GH actions using containers for some nextflow pipelines under a (free (?)) organization account - so far, I have not encountered problems with GH actions (e.g. clean and CoVpipe2). But I have to say that I have no overview of the limits, especially with non-organization accounts
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Related Issues (20)
- add skip scorpio parameter to pangolin HOT 1
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
- Test Freyja Update function HOT 11
- Singularity container execution of pangolin crashes with recent nextflow versions HOT 6
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