Gzi input for mutect2 #9043
Gzi input for mutect2 #9043
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the mitochondria test was really fast which was the reason why I chose this test with the gzi input to ensure the input runs
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You can join the org by jumping on slack and writing in #github-invitations (https://nf-co.re/join) |
.idea/.gitignore
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please remove all the .idea/... files from the PR :)
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@famosab gotcha thank you for the feedback will implement those changes soon! |
| "human - bam - generate_pon": { | ||
| "content": [ | ||
| "876aa6be01c0c8fc71ad8e99ed842240", | ||
| "c3b555d00c575478b65626f56e3085c4", |
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any idea why all of these md5sums change even though we changed nothing about thr module itself? 🤔
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i ran the tests for other modules since i was moving the inputs around
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but still the bam readsMD5 sum should not change just because you add an empty input
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@apetizerr You will also need to adapt the subworkflows to make the tests pass as we add a new input here they fail. The following subworkflows need to be updated:
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| "human - cram": { | ||
| "content": [ | ||
| "1b65f1a163b517944bf2e4b74230e035", | ||
| "6a839307b251fbeb1a4b08e3b3692513", |
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I think these changes should not have happened - I guess that they are due to the platform you ran the tests on. I had these issues sometimes when running directly on my mac. We have multiple possibilities to solve this: either switch to a linux workstation or run it in gitpod :)
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It looks good but I think you need to run the tests again on gitpod or a different environment or otherwise the tests will fail because the checksums do not match |
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Yeah the tests are failing because some of the md5sums changed when you ran it locally (this should not happen for tests that you do not touch). I would suggest to try an run it in gitpod :) |
- Updated snapshots for all test cases with current GATK4 v4.6.2.0 - Tests run with Docker profile to ensure reproducibility - Updated timestamps to 2025-10-02 - All tests passing with updated snapshots Co-authored-by: Ona <[email protected]>
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tests ran via ona/gitpod |
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Ok lets see if the tests run. In the meantime did you request to be added to the github org in the slack? Maybe you can do that then for the next PR you can directly see the CI tests :) |
| "timestamp": "2025-09-15T16:17:00.767220472" | ||
| "timestamp": "2025-09-14T23:49:18.290784" | ||
| }, | ||
| "human - bam - tumor_normal_pair_f1r2 - stub": { |
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Now the results for this test are completely empty....
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I requested to join the github org and invited to give access
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Since there is a limit to the number of times i can use ONA to test, should I set up my environment in windows OS and not mac to avoid the checksum troubles?
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No I think either we use linux or I will try and run it on my linux workstation locally
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nf-core/modules pull request
PR checklist
Closes #8789
versions.ymlfile.bugnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda