WIP: Nf test conversion: shortDNA #1144
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Metagenomics section still needs tweaking, but the rest seems consistent. Try again on a different day to ensure no timestamps are used also. |
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Tests are done, double check on another day required |
TCLamnidis
approved these changes
Sep 12, 2025
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ToDos:
- merge latest changes from
dev(includes new nf-core template) - Add profile tag to the test so it works with the new CI runner
- Update commands in the instructions for how to update the test in future
- Update snapshots to work with latest template (MultiQC got a version bump)
- Rename test to match new naming scheme
- exclude preseq command log from md5sum checks
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| tag "test_shortdna" | ||
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| tag "test_shortdna" | |
| tag "test_shortdna" | |
| profile "test_shortdna" |
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| // Generate with: nf-test test --tag test --profile docker,test --update-snapshot | ||
| // Test with: nf-test test --tag test --profile docker,test |
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| // Generate with: nf-test test --tag test --profile docker,test --update-snapshot | |
| // Test with: nf-test test --tag test --profile docker,test | |
| // Generate with: nf-test test --profile +docker --tag test_shortdna --update-snapshot | |
| // Test with: nf-test test --profile +docker --tag test_shortdna |
TCLamnidis
reviewed
Sep 12, 2025
| tag "nfcore_eager" | ||
| tag "test_shortdna" | ||
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| test("test_shortdna_profile") { |
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| test("test_shortdna_profile") { | |
| test("Test `test_shortdna` profile:") { |
TCLamnidis
reviewed
Sep 12, 2025
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| "**/mapping_quality_histogram.txt", | ||
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| "**/mapping_quality_histogram.txt", | |
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| "**/mapping_quality_histogram.txt", | |
| '**/*command.log', | |
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PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).This is the PR for Issue #1135