Set use_work_dir_as_temp to true when running at the Sanger

muffato commented 10 months ago

I'm not 100% sure it's what caused the issue with /tmp yesterday, but it's definitely something that I forgot to set.

What do you think of the implementation ?

I put it in conf/test_full.config because this config file is already Sanger-specific
Therefore I don't need to put it in .github/workflows/sanger_test_full.yml
But I still need to put it in .github/workflows/sanger_test.yml because this one is using the "test" profile
I don't update the "test" profile because it's meant to be used by anyone, incl. on GitHub, and we don't want to enforce use_work_dir_as_temp to them. Also, the data are small enough that is shouldn't matter on the farm

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 10 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit e5bb165

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

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Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - 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gq1 commented 10 months ago

Probably we don't need use_work_dir_as_temp to be true for test profile when running on the farm.

Manually triggered both Sanger Github workflows and we can see use_work_dir_as_temp = true in the parameters file now, previously for the failed job use_work_dir_as_temp = false.

gq1 commented 10 months ago

I manually trigger the full test on the farm again and hope this time it will succeed even if with use_work_dir_as_temp = false.

Otherwise, we only have half results on the pipeline webpages: https://pipelines.tol.sanger.ac.uk/genomenote/results#genomenote/results-81c53c6657c377c7d6b7a11085779a8a4d67839e/

The readmapping release run is fine. https://pipelines.tol.sanger.ac.uk/readmapping/results#readmapping/results-91efc18ea1c3d504f75502af47e83f630e0b48d5/

gq1 commented 10 months ago

I manually trigger the full test on the farm again and hope this time it will succeed even if with use_work_dir_as_temp = false. The run succeeded this time. https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/4PYhtmuWyfgplG

Otherwise, we only have half results on the pipeline webpages: https://pipelines.tol.sanger.ac.uk/genomenote/results#genomenote/results-81c53c6657c377c7d6b7a11085779a8a4d67839e/

Hope the results will be updated tomorrow.

sanger-tol / genomenote