Fix CI issues #96
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Fix CI issues #96
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Joon-Klaps
reviewed
Jun 20, 2025
tests/default.nf.test
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| ).match() }, | ||
| { assert using_conda || snapshot( | ||
| // Number of successful tasks | ||
| workflow.trace.succeeded().size(), | ||
| // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions | ||
| removeNextflowVersion("$outputDir/pipeline_info/nf_core_reportho_software_mqc_versions.yml"), | ||
| // All report stable path name, with a relative path | ||
| report_stable_name, | ||
| // All report files with stable contents | ||
| report_stable_path | ||
| ).match() } |
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Did you test this? conda tests did not run on ci. I think you might need two different snapshot names for match as they could overwrite each other.
ie .match("default profile") and .match("conda profile")
Joon-Klaps
reviewed
Jun 20, 2025
Joon-Klaps
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Most of it looks good to me, but couple of things you might want to double check.
tests/default.nf.test
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| ).match() }, | ||
| { assert using_conda || snapshot( | ||
| // Number of successful tasks | ||
| workflow.trace.succeeded().size(), | ||
| // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions | ||
| removeNextflowVersion("$outputDir/pipeline_info/nf_core_reportho_software_mqc_versions.yml"), | ||
| // All report stable path name, with a relative path | ||
| report_stable_name, | ||
| // All report files with stable contents | ||
| report_stable_path |
tests/default.nf.test
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| def report_stable_name = getAllFilesFromDir("$outputDir/report", relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) | ||
| def report_stable_path = getAllFilesFromDir("$outputDir/report", ignoreFile: 'tests/.nftignore') |
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Maybe be consistent with params.outdir
| then { | ||
| // stable_name: All files + folders in ${params.outdir}/ with a stable name | ||
| def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) | ||
| def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'report', 'report/**']) |
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Was this deliberate? Looking at the snapshot almost all file names are removed.
Collaborator
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Hi @Joon-Klaps, thanks for the review! It's great that you've noticed the issue. I've investigated, and it turns out that the non-Conda CI never runs. I'll need to find a better way to detect Conda runs, although it won't be easy, as I've already tried several and none worked correctly. |
Collaborator
Author
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Hi @Joon-Klaps, after consultation with the other maintainers I've decided to give up on Conda tests for the upcoming release. I would appreciate a re-review. |
Joon-Klaps
approved these changes
Jul 3, 2025
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Fix several CI issues:
defaultsin the old versionThere might be some
nf-core pipelines downloadissues left in the release CI after this PRPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).